{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Exercise 6.4: Filter, extract, rinse, repeat\n", "\n", "This exercise was written in collaboration with Griffin Chure.\n", "\n", "
" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "So far we have seen that in a single (very clean) image, we can get somewhere around 20 - 30 well-separated cells in a single 100$\\times$ magnification phase contrast image. However, if you wish to report a mean fluorescence intensity for a single strain, you would certainly want more cells to have a good degree of confidence. Using the principles you learned above, your job will be to report a mean fluorescence value for the HG105 *E. coli* strain using **all** of the images located in `data/HG105_images/`. To do this, you should do the following:\n", "\n", "1. Get a list of all of the image files in `~/git/data/HG105_images/`.\n", "2. Separate them by phase contrast (for segmentation) and FITC (for measurement). \n", "3. Iterate through each image file and perform segmentation and fluorescence intensity extraction for each cell. These values should be stored in a NumPy array or Pandas `DataFrame`. \n", "4. Plot an ECDF of all extracted fluorescence intensities and report a mean and standard deviation as well as the number of cells you successfully measured. \n", "5. Obtain 95% bootstrap confidence intervals for the mean and standard deviation of the fluorescence intensities.\n", "\n", "As a reminder, the interpixel distance of these images is 0.0626 µm per pixel." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Solution\n", "\n", "
" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "data": { "application/javascript": [ "(function(root) {\n", " function now() {\n", " return new Date();\n", " }\n", "\n", " var force = true;\n", " var py_version = '3.1.1'.replace('rc', '-rc.');\n", " var is_dev = py_version.indexOf(\"+\") !== -1 || py_version.indexOf(\"-\") !== -1;\n", " var reloading = false;\n", " var Bokeh = root.Bokeh;\n", " var bokeh_loaded = Bokeh != null && (Bokeh.version === py_version || (Bokeh.versions !== undefined && Bokeh.versions.has(py_version)));\n", "\n", " if (typeof (root._bokeh_timeout) === \"undefined\" || force) {\n", " root._bokeh_timeout = Date.now() + 5000;\n", " root._bokeh_failed_load = false;\n", " }\n", "\n", " function run_callbacks() {\n", " try {\n", " root._bokeh_onload_callbacks.forEach(function(callback) {\n", " if (callback != null)\n", " callback();\n", " });\n", " } finally {\n", " delete root._bokeh_onload_callbacks;\n", " }\n", " console.debug(\"Bokeh: all callbacks have finished\");\n", " }\n", "\n", " function load_libs(css_urls, js_urls, js_modules, js_exports, callback) {\n", " if (css_urls == null) css_urls = [];\n", " if (js_urls == null) js_urls = [];\n", " if (js_modules == null) js_modules = [];\n", " if (js_exports == null) js_exports = {};\n", "\n", " root._bokeh_onload_callbacks.push(callback);\n", "\n", " if (root._bokeh_is_loading > 0) {\n", " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", " return null;\n", " }\n", " if (js_urls.length === 0 && js_modules.length === 0 && Object.keys(js_exports).length === 0) {\n", " run_callbacks();\n", " return null;\n", " }\n", " if (!reloading) {\n", " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", " }\n", "\n", " function on_load() {\n", " root._bokeh_is_loading--;\n", " if (root._bokeh_is_loading === 0) {\n", " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", " run_callbacks()\n", " }\n", " }\n", " window._bokeh_on_load = on_load\n", "\n", " function on_error() {\n", " console.error(\"failed to load \" + url);\n", " }\n", "\n", " var skip = [];\n", " if (window.requirejs) {\n", " window.requirejs.config({'packages': {}, 'paths': {'jspanel': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/jspanel', 'jspanel-modal': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/modal/jspanel.modal', 'jspanel-tooltip': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/tooltip/jspanel.tooltip', 'jspanel-hint': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/hint/jspanel.hint', 'jspanel-layout': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/layout/jspanel.layout', 'jspanel-contextmenu': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/contextmenu/jspanel.contextmenu', 'jspanel-dock': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/dock/jspanel.dock', 'gridstack': 'https://cdn.jsdelivr.net/npm/gridstack@7.2.3/dist/gridstack-all', 'notyf': 'https://cdn.jsdelivr.net/npm/notyf@3/notyf.min'}, 'shim': {'jspanel': {'exports': 'jsPanel'}, 'gridstack': {'exports': 'GridStack'}}});\n", " require([\"jspanel\"], function(jsPanel) {\n", "\twindow.jsPanel = jsPanel\n", "\ton_load()\n", " })\n", " require([\"jspanel-modal\"], function() {\n", "\ton_load()\n", " })\n", " require([\"jspanel-tooltip\"], function() {\n", "\ton_load()\n", " })\n", " require([\"jspanel-hint\"], function() {\n", "\ton_load()\n", " })\n", " require([\"jspanel-layout\"], function() {\n", "\ton_load()\n", " })\n", " require([\"jspanel-contextmenu\"], function() {\n", "\ton_load()\n", " })\n", " require([\"jspanel-dock\"], function() {\n", "\ton_load()\n", " })\n", " require([\"gridstack\"], function(GridStack) {\n", "\twindow.GridStack = GridStack\n", "\ton_load()\n", " })\n", " require([\"notyf\"], function() {\n", "\ton_load()\n", " })\n", " root._bokeh_is_loading = css_urls.length + 9;\n", " } else {\n", " root._bokeh_is_loading = css_urls.length + js_urls.length + js_modules.length + Object.keys(js_exports).length;\n", " }\n", "\n", " var existing_stylesheets = []\n", " var links = document.getElementsByTagName('link')\n", " for (var i = 0; i < links.length; i++) {\n", " var link = links[i]\n", " if (link.href != null) {\n", "\texisting_stylesheets.push(link.href)\n", " }\n", " }\n", " for (var i = 0; i < css_urls.length; i++) {\n", " var url = css_urls[i];\n", " if (existing_stylesheets.indexOf(url) !== -1) {\n", "\ton_load()\n", "\tcontinue;\n", " }\n", " const element = document.createElement(\"link\");\n", " element.onload = on_load;\n", " element.onerror = on_error;\n", " element.rel = \"stylesheet\";\n", " element.type = \"text/css\";\n", " element.href = url;\n", " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", " document.body.appendChild(element);\n", " } if (((window['jsPanel'] !== undefined) && (!(window['jsPanel'] instanceof HTMLElement))) || window.requirejs) {\n", " var urls = ['https://cdn.holoviz.org/panel/1.1.0/dist/bundled/floatpanel/jspanel4@4.12.0/dist/jspanel.js', 'https://cdn.holoviz.org/panel/1.1.0/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/modal/jspanel.modal.js', 'https://cdn.holoviz.org/panel/1.1.0/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/tooltip/jspanel.tooltip.js', 'https://cdn.holoviz.org/panel/1.1.0/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/hint/jspanel.hint.js', 'https://cdn.holoviz.org/panel/1.1.0/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/layout/jspanel.layout.js', 'https://cdn.holoviz.org/panel/1.1.0/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/contextmenu/jspanel.contextmenu.js', 'https://cdn.holoviz.org/panel/1.1.0/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/dock/jspanel.dock.js'];\n", " for (var i = 0; i < urls.length; i++) {\n", " skip.push(urls[i])\n", " }\n", " } if (((window['GridStack'] !== undefined) && (!(window['GridStack'] instanceof HTMLElement))) || window.requirejs) {\n", " var urls = ['https://cdn.holoviz.org/panel/1.1.0/dist/bundled/gridstack/gridstack@7.2.3/dist/gridstack-all.js'];\n", " for (var i = 0; i < urls.length; i++) {\n", " skip.push(urls[i])\n", " }\n", " } if (((window['Notyf'] !== undefined) && (!(window['Notyf'] instanceof HTMLElement))) || window.requirejs) {\n", " var urls = ['https://cdn.holoviz.org/panel/1.1.0/dist/bundled/notificationarea/notyf@3/notyf.min.js'];\n", " for (var i = 0; i < urls.length; i++) {\n", " skip.push(urls[i])\n", " }\n", " } var existing_scripts = []\n", " var scripts = document.getElementsByTagName('script')\n", " for (var i = 0; i < scripts.length; i++) {\n", " var script = scripts[i]\n", " if (script.src != null) {\n", "\texisting_scripts.push(script.src)\n", " }\n", " }\n", " for (var i = 0; i < js_urls.length; i++) {\n", " var url = js_urls[i];\n", " if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n", "\tif (!window.requirejs) {\n", "\t on_load();\n", "\t}\n", "\tcontinue;\n", " }\n", " var element = document.createElement('script');\n", " element.onload = on_load;\n", " element.onerror = on_error;\n", " element.async = false;\n", " element.src = url;\n", " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " document.head.appendChild(element);\n", " }\n", " for (var i = 0; i < js_modules.length; i++) {\n", " var url = js_modules[i];\n", " if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n", "\tif (!window.requirejs) {\n", "\t on_load();\n", "\t}\n", "\tcontinue;\n", " }\n", " var element = document.createElement('script');\n", " element.onload = on_load;\n", " element.onerror = on_error;\n", " element.async = false;\n", " element.src = url;\n", " element.type = \"module\";\n", " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " document.head.appendChild(element);\n", " }\n", " for (const name in js_exports) {\n", " var url = js_exports[name];\n", " if (skip.indexOf(url) >= 0 || root[name] != null) {\n", "\tif (!window.requirejs) {\n", "\t on_load();\n", "\t}\n", "\tcontinue;\n", " }\n", " var element = document.createElement('script');\n", " element.onerror = on_error;\n", " element.async = false;\n", " element.type = \"module\";\n", " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " element.textContent = `\n", " import ${name} from \"${url}\"\n", " window.${name} = ${name}\n", " window._bokeh_on_load()\n", " `\n", " document.head.appendChild(element);\n", " }\n", " if (!js_urls.length && !js_modules.length) {\n", " on_load()\n", " }\n", " };\n", "\n", " function inject_raw_css(css) {\n", " const element = document.createElement(\"style\");\n", " element.appendChild(document.createTextNode(css));\n", " document.body.appendChild(element);\n", " }\n", "\n", " var js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.1.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.1.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.1.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.1.1.min.js\", \"https://cdn.holoviz.org/panel/1.1.0/dist/panel.min.js\"];\n", " var js_modules = [];\n", " var js_exports = {};\n", " var css_urls = [];\n", " var inline_js = [ function(Bokeh) {\n", " Bokeh.set_log_level(\"info\");\n", " },\n", "function(Bokeh) {} // ensure no trailing comma for IE\n", " ];\n", "\n", " function run_inline_js() {\n", " if ((root.Bokeh !== undefined) || (force === true)) {\n", " for (var i = 0; i < inline_js.length; i++) {\n", " inline_js[i].call(root, root.Bokeh);\n", " }\n", " // Cache old bokeh versions\n", " if (Bokeh != undefined && !reloading) {\n", "\tvar NewBokeh = root.Bokeh;\n", "\tif (Bokeh.versions === undefined) {\n", "\t Bokeh.versions = new Map();\n", "\t}\n", "\tif (NewBokeh.version !== Bokeh.version) {\n", "\t Bokeh.versions.set(NewBokeh.version, NewBokeh)\n", "\t}\n", "\troot.Bokeh = Bokeh;\n", " }} else if (Date.now() < root._bokeh_timeout) {\n", " setTimeout(run_inline_js, 100);\n", " } else if (!root._bokeh_failed_load) {\n", " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", " root._bokeh_failed_load = true;\n", " }\n", " root._bokeh_is_initializing = false\n", " }\n", "\n", " function load_or_wait() {\n", " // Implement a backoff loop that tries to ensure we do not load multiple\n", " // versions of Bokeh and its dependencies at the same time.\n", " // In recent versions we use the root._bokeh_is_initializing flag\n", " // to determine whether there is an ongoing attempt to initialize\n", " // bokeh, however for backward compatibility we also try to ensure\n", " // that we do not start loading a newer (Panel>=1.0 and Bokeh>3) version\n", " // before older versions are fully initialized.\n", " if (root._bokeh_is_initializing && Date.now() > root._bokeh_timeout) {\n", " root._bokeh_is_initializing = false;\n", " root._bokeh_onload_callbacks = undefined;\n", " console.log(\"Bokeh: BokehJS was loaded multiple times but one version failed to initialize.\");\n", " load_or_wait();\n", " } else if (root._bokeh_is_initializing || (typeof root._bokeh_is_initializing === \"undefined\" && root._bokeh_onload_callbacks !== undefined)) {\n", " setTimeout(load_or_wait, 100);\n", " } else {\n", " Bokeh = root.Bokeh;\n", " bokeh_loaded = Bokeh != null && (Bokeh.version === py_version || (Bokeh.versions !== undefined && Bokeh.versions.has(py_version)));\n", " root._bokeh_is_initializing = true\n", " root._bokeh_onload_callbacks = []\n", " if (!reloading && (!bokeh_loaded || is_dev)) {\n", "\troot.Bokeh = undefined;\n", " }\n", " load_libs(css_urls, js_urls, js_modules, js_exports, function() {\n", "\tconsole.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", "\trun_inline_js();\n", " });\n", " }\n", " }\n", " // Give older versions of the autoload script a head-start to ensure\n", " // they initialize before we start loading newer version.\n", " setTimeout(load_or_wait, 100)\n", "}(window));" ], "application/vnd.holoviews_load.v0+json": "(function(root) {\n function now() {\n return new Date();\n }\n\n var force = true;\n var py_version = '3.1.1'.replace('rc', '-rc.');\n var is_dev = py_version.indexOf(\"+\") !== -1 || py_version.indexOf(\"-\") !== -1;\n var reloading = false;\n var Bokeh = root.Bokeh;\n var bokeh_loaded = Bokeh != null && (Bokeh.version === py_version || (Bokeh.versions !== undefined && Bokeh.versions.has(py_version)));\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks;\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, js_modules, js_exports, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n if (js_modules == null) js_modules = [];\n if (js_exports == null) js_exports = {};\n\n root._bokeh_onload_callbacks.push(callback);\n\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls.length === 0 && js_modules.length === 0 && Object.keys(js_exports).length === 0) {\n run_callbacks();\n return null;\n }\n if (!reloading) {\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n }\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n window._bokeh_on_load = on_load\n\n function on_error() {\n console.error(\"failed to load \" + url);\n }\n\n var skip = [];\n if (window.requirejs) {\n window.requirejs.config({'packages': {}, 'paths': {'jspanel': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/jspanel', 'jspanel-modal': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/modal/jspanel.modal', 'jspanel-tooltip': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/tooltip/jspanel.tooltip', 'jspanel-hint': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/hint/jspanel.hint', 'jspanel-layout': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/layout/jspanel.layout', 'jspanel-contextmenu': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/contextmenu/jspanel.contextmenu', 'jspanel-dock': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/dock/jspanel.dock', 'gridstack': 'https://cdn.jsdelivr.net/npm/gridstack@7.2.3/dist/gridstack-all', 'notyf': 'https://cdn.jsdelivr.net/npm/notyf@3/notyf.min'}, 'shim': {'jspanel': {'exports': 'jsPanel'}, 'gridstack': {'exports': 'GridStack'}}});\n require([\"jspanel\"], function(jsPanel) {\n\twindow.jsPanel = jsPanel\n\ton_load()\n })\n require([\"jspanel-modal\"], function() {\n\ton_load()\n })\n require([\"jspanel-tooltip\"], function() {\n\ton_load()\n })\n require([\"jspanel-hint\"], function() {\n\ton_load()\n })\n require([\"jspanel-layout\"], function() {\n\ton_load()\n })\n require([\"jspanel-contextmenu\"], function() {\n\ton_load()\n })\n require([\"jspanel-dock\"], function() {\n\ton_load()\n })\n require([\"gridstack\"], function(GridStack) {\n\twindow.GridStack = GridStack\n\ton_load()\n })\n require([\"notyf\"], function() {\n\ton_load()\n })\n root._bokeh_is_loading = css_urls.length + 9;\n } else {\n root._bokeh_is_loading = css_urls.length + js_urls.length + js_modules.length + Object.keys(js_exports).length;\n }\n\n var existing_stylesheets = []\n var links = document.getElementsByTagName('link')\n for (var i = 0; i < links.length; i++) {\n var link = links[i]\n if (link.href != null) {\n\texisting_stylesheets.push(link.href)\n }\n }\n for (var i = 0; i < css_urls.length; i++) {\n var url = css_urls[i];\n if (existing_stylesheets.indexOf(url) !== -1) {\n\ton_load()\n\tcontinue;\n }\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error;\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n } if (((window['jsPanel'] !== undefined) && (!(window['jsPanel'] instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.1.0/dist/bundled/floatpanel/jspanel4@4.12.0/dist/jspanel.js', 'https://cdn.holoviz.org/panel/1.1.0/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/modal/jspanel.modal.js', 'https://cdn.holoviz.org/panel/1.1.0/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/tooltip/jspanel.tooltip.js', 'https://cdn.holoviz.org/panel/1.1.0/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/hint/jspanel.hint.js', 'https://cdn.holoviz.org/panel/1.1.0/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/layout/jspanel.layout.js', 'https://cdn.holoviz.org/panel/1.1.0/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/contextmenu/jspanel.contextmenu.js', 'https://cdn.holoviz.org/panel/1.1.0/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/dock/jspanel.dock.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window['GridStack'] !== undefined) && (!(window['GridStack'] instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.1.0/dist/bundled/gridstack/gridstack@7.2.3/dist/gridstack-all.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window['Notyf'] !== undefined) && (!(window['Notyf'] instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.1.0/dist/bundled/notificationarea/notyf@3/notyf.min.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } var existing_scripts = []\n var scripts = document.getElementsByTagName('script')\n for (var i = 0; i < scripts.length; i++) {\n var script = scripts[i]\n if (script.src != null) {\n\texisting_scripts.push(script.src)\n }\n }\n for (var i = 0; i < js_urls.length; i++) {\n var url = js_urls[i];\n if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n\tif (!window.requirejs) {\n\t on_load();\n\t}\n\tcontinue;\n }\n var element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error;\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n for (var i = 0; i < js_modules.length; i++) {\n var url = js_modules[i];\n if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n\tif (!window.requirejs) {\n\t on_load();\n\t}\n\tcontinue;\n }\n var element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error;\n element.async = false;\n element.src = url;\n element.type = \"module\";\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n for (const name in js_exports) {\n var url = js_exports[name];\n if (skip.indexOf(url) >= 0 || root[name] != null) {\n\tif (!window.requirejs) {\n\t on_load();\n\t}\n\tcontinue;\n }\n var element = document.createElement('script');\n element.onerror = on_error;\n element.async = false;\n element.type = \"module\";\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n element.textContent = `\n import ${name} from \"${url}\"\n window.${name} = ${name}\n window._bokeh_on_load()\n `\n document.head.appendChild(element);\n }\n if (!js_urls.length && !js_modules.length) {\n on_load()\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n var js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.1.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.1.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.1.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.1.1.min.js\", \"https://cdn.holoviz.org/panel/1.1.0/dist/panel.min.js\"];\n var js_modules = [];\n var js_exports = {};\n var css_urls = [];\n var inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {} // ensure no trailing comma for IE\n ];\n\n function run_inline_js() {\n if ((root.Bokeh !== undefined) || (force === true)) {\n for (var i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n // Cache old bokeh versions\n if (Bokeh != undefined && !reloading) {\n\tvar NewBokeh = root.Bokeh;\n\tif (Bokeh.versions === undefined) {\n\t Bokeh.versions = new Map();\n\t}\n\tif (NewBokeh.version !== Bokeh.version) {\n\t Bokeh.versions.set(NewBokeh.version, NewBokeh)\n\t}\n\troot.Bokeh = Bokeh;\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n }\n root._bokeh_is_initializing = false\n }\n\n function load_or_wait() {\n // Implement a backoff loop that tries to ensure we do not load multiple\n // versions of Bokeh and its dependencies at the same time.\n // In recent versions we use the root._bokeh_is_initializing flag\n // to determine whether there is an ongoing attempt to initialize\n // bokeh, however for backward compatibility we also try to ensure\n // that we do not start loading a newer (Panel>=1.0 and Bokeh>3) version\n // before older versions are fully initialized.\n if (root._bokeh_is_initializing && Date.now() > root._bokeh_timeout) {\n root._bokeh_is_initializing = false;\n root._bokeh_onload_callbacks = undefined;\n console.log(\"Bokeh: BokehJS was loaded multiple times but one version failed to initialize.\");\n load_or_wait();\n } else if (root._bokeh_is_initializing || (typeof root._bokeh_is_initializing === \"undefined\" && root._bokeh_onload_callbacks !== undefined)) {\n setTimeout(load_or_wait, 100);\n } else {\n Bokeh = root.Bokeh;\n bokeh_loaded = Bokeh != null && (Bokeh.version === py_version || (Bokeh.versions !== undefined && Bokeh.versions.has(py_version)));\n root._bokeh_is_initializing = true\n root._bokeh_onload_callbacks = []\n if (!reloading && (!bokeh_loaded || is_dev)) {\n\troot.Bokeh = undefined;\n }\n load_libs(css_urls, js_urls, js_modules, js_exports, function() {\n\tconsole.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n\trun_inline_js();\n });\n }\n }\n // Give older versions of the autoload script a head-start to ensure\n // they initialize before we start loading newer version.\n setTimeout(load_or_wait, 100)\n}(window));" }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "\n", "if ((window.PyViz === undefined) || (window.PyViz instanceof HTMLElement)) {\n", " window.PyViz = {comms: {}, comm_status:{}, kernels:{}, receivers: {}, plot_index: []}\n", "}\n", "\n", "\n", " function JupyterCommManager() {\n", " }\n", "\n", " JupyterCommManager.prototype.register_target = function(plot_id, comm_id, msg_handler) {\n", " if (window.comm_manager || ((window.Jupyter !== undefined) && (Jupyter.notebook.kernel != null))) {\n", " var comm_manager = window.comm_manager || Jupyter.notebook.kernel.comm_manager;\n", " comm_manager.register_target(comm_id, function(comm) {\n", " comm.on_msg(msg_handler);\n", " });\n", " } else if ((plot_id in window.PyViz.kernels) && (window.PyViz.kernels[plot_id])) {\n", " window.PyViz.kernels[plot_id].registerCommTarget(comm_id, function(comm) {\n", " comm.onMsg = msg_handler;\n", " });\n", " } else if (typeof google != 'undefined' && google.colab.kernel != null) {\n", " google.colab.kernel.comms.registerTarget(comm_id, (comm) => {\n", " var messages = comm.messages[Symbol.asyncIterator]();\n", " function processIteratorResult(result) {\n", " var message = result.value;\n", " console.log(message)\n", " var content = {data: message.data, comm_id};\n", " var buffers = []\n", " for (var buffer of message.buffers || []) {\n", " buffers.push(new DataView(buffer))\n", " }\n", " var metadata = message.metadata || {};\n", " var msg = {content, buffers, metadata}\n", " msg_handler(msg);\n", " return messages.next().then(processIteratorResult);\n", " }\n", " return messages.next().then(processIteratorResult);\n", " })\n", " }\n", " }\n", "\n", " JupyterCommManager.prototype.get_client_comm = function(plot_id, comm_id, msg_handler) {\n", " if (comm_id in window.PyViz.comms) {\n", " return window.PyViz.comms[comm_id];\n", " } else if (window.comm_manager || ((window.Jupyter !== undefined) && (Jupyter.notebook.kernel != null))) {\n", " var comm_manager = window.comm_manager || Jupyter.notebook.kernel.comm_manager;\n", " var comm = comm_manager.new_comm(comm_id, {}, {}, {}, comm_id);\n", " if (msg_handler) {\n", " comm.on_msg(msg_handler);\n", " }\n", " } else if ((plot_id in window.PyViz.kernels) && (window.PyViz.kernels[plot_id])) {\n", " var comm = window.PyViz.kernels[plot_id].connectToComm(comm_id);\n", " comm.open();\n", " if (msg_handler) {\n", " comm.onMsg = msg_handler;\n", " }\n", " } else if (typeof google != 'undefined' && google.colab.kernel != null) {\n", " var comm_promise = google.colab.kernel.comms.open(comm_id)\n", " comm_promise.then((comm) => {\n", " window.PyViz.comms[comm_id] = comm;\n", " if (msg_handler) {\n", " var messages = comm.messages[Symbol.asyncIterator]();\n", " function processIteratorResult(result) {\n", " var message = result.value;\n", " var content = {data: message.data};\n", " var metadata = message.metadata || {comm_id};\n", " var msg = {content, metadata}\n", " msg_handler(msg);\n", " return messages.next().then(processIteratorResult);\n", " }\n", " return messages.next().then(processIteratorResult);\n", " }\n", " }) \n", " var sendClosure = (data, metadata, buffers, disposeOnDone) => {\n", " return comm_promise.then((comm) => {\n", " comm.send(data, metadata, buffers, disposeOnDone);\n", " });\n", " };\n", " var comm = {\n", " send: sendClosure\n", " };\n", " }\n", " window.PyViz.comms[comm_id] = comm;\n", " return comm;\n", " }\n", " window.PyViz.comm_manager = new JupyterCommManager();\n", " \n", "\n", "\n", "var JS_MIME_TYPE = 'application/javascript';\n", "var HTML_MIME_TYPE = 'text/html';\n", "var EXEC_MIME_TYPE = 'application/vnd.holoviews_exec.v0+json';\n", "var CLASS_NAME = 'output';\n", "\n", "/**\n", " * Render data to the DOM node\n", " */\n", "function render(props, node) {\n", " var div = document.createElement(\"div\");\n", " var script = document.createElement(\"script\");\n", " node.appendChild(div);\n", " node.appendChild(script);\n", "}\n", "\n", "/**\n", " * Handle when a new output is added\n", " */\n", "function handle_add_output(event, handle) {\n", " var output_area = handle.output_area;\n", " var output = handle.output;\n", " if ((output.data == undefined) || (!output.data.hasOwnProperty(EXEC_MIME_TYPE))) {\n", " return\n", " }\n", " var id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", " var toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", " if (id !== undefined) {\n", " var nchildren = toinsert.length;\n", " var html_node = toinsert[nchildren-1].children[0];\n", " html_node.innerHTML = output.data[HTML_MIME_TYPE];\n", " var scripts = [];\n", " var nodelist = html_node.querySelectorAll(\"script\");\n", " for (var i in nodelist) {\n", " if (nodelist.hasOwnProperty(i)) {\n", " scripts.push(nodelist[i])\n", " }\n", " }\n", "\n", " scripts.forEach( function (oldScript) {\n", " var newScript = document.createElement(\"script\");\n", " var attrs = [];\n", " var nodemap = oldScript.attributes;\n", " for (var j in nodemap) {\n", " if (nodemap.hasOwnProperty(j)) {\n", " attrs.push(nodemap[j])\n", " }\n", " }\n", " attrs.forEach(function(attr) { newScript.setAttribute(attr.name, attr.value) });\n", " newScript.appendChild(document.createTextNode(oldScript.innerHTML));\n", " oldScript.parentNode.replaceChild(newScript, oldScript);\n", " });\n", " if (JS_MIME_TYPE in output.data) {\n", " toinsert[nchildren-1].children[1].textContent = output.data[JS_MIME_TYPE];\n", " }\n", " output_area._hv_plot_id = id;\n", " if ((window.Bokeh !== undefined) && (id in Bokeh.index)) {\n", " window.PyViz.plot_index[id] = Bokeh.index[id];\n", " } else {\n", " window.PyViz.plot_index[id] = null;\n", " }\n", " } else if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", " var bk_div = document.createElement(\"div\");\n", " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", " var script_attrs = bk_div.children[0].attributes;\n", " for (var i = 0; i < script_attrs.length; i++) {\n", " toinsert[toinsert.length - 1].childNodes[1].setAttribute(script_attrs[i].name, script_attrs[i].value);\n", " }\n", " // store reference to server id on output_area\n", " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", " }\n", "}\n", "\n", "/**\n", " * Handle when an output is cleared or removed\n", " */\n", "function handle_clear_output(event, handle) {\n", " var id = handle.cell.output_area._hv_plot_id;\n", " var server_id = handle.cell.output_area._bokeh_server_id;\n", " if (((id === undefined) || !(id in PyViz.plot_index)) && (server_id !== undefined)) { return; }\n", " var comm = window.PyViz.comm_manager.get_client_comm(\"hv-extension-comm\", \"hv-extension-comm\", function () {});\n", " if (server_id !== null) {\n", " comm.send({event_type: 'server_delete', 'id': server_id});\n", " return;\n", " } else if (comm !== null) {\n", " comm.send({event_type: 'delete', 'id': id});\n", " }\n", " delete PyViz.plot_index[id];\n", " if ((window.Bokeh !== undefined) & (id in window.Bokeh.index)) {\n", " var doc = window.Bokeh.index[id].model.document\n", " doc.clear();\n", " const i = window.Bokeh.documents.indexOf(doc);\n", " if (i > -1) {\n", " window.Bokeh.documents.splice(i, 1);\n", " }\n", " }\n", "}\n", "\n", "/**\n", " * Handle kernel restart event\n", " */\n", "function handle_kernel_cleanup(event, handle) {\n", " delete PyViz.comms[\"hv-extension-comm\"];\n", " window.PyViz.plot_index = {}\n", "}\n", "\n", "/**\n", " * Handle update_display_data messages\n", " */\n", "function handle_update_output(event, handle) {\n", " handle_clear_output(event, {cell: {output_area: handle.output_area}})\n", " handle_add_output(event, handle)\n", "}\n", "\n", "function register_renderer(events, OutputArea) {\n", " function append_mime(data, metadata, element) {\n", " // create a DOM node to render to\n", " var toinsert = this.create_output_subarea(\n", " metadata,\n", " CLASS_NAME,\n", " EXEC_MIME_TYPE\n", " );\n", " this.keyboard_manager.register_events(toinsert);\n", " // Render to node\n", " var props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", " render(props, toinsert[0]);\n", " element.append(toinsert);\n", " return toinsert\n", " }\n", "\n", " events.on('output_added.OutputArea', handle_add_output);\n", " events.on('output_updated.OutputArea', handle_update_output);\n", " events.on('clear_output.CodeCell', handle_clear_output);\n", " events.on('delete.Cell', handle_clear_output);\n", " events.on('kernel_ready.Kernel', handle_kernel_cleanup);\n", "\n", " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", " safe: true,\n", " index: 0\n", " });\n", "}\n", "\n", "if (window.Jupyter !== undefined) {\n", " try {\n", " var events = require('base/js/events');\n", " var OutputArea = require('notebook/js/outputarea').OutputArea;\n", " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", " register_renderer(events, OutputArea);\n", " }\n", " } catch(err) {\n", " }\n", "}\n" ], "application/vnd.holoviews_load.v0+json": "\nif ((window.PyViz === undefined) || (window.PyViz instanceof HTMLElement)) {\n window.PyViz = {comms: {}, comm_status:{}, kernels:{}, receivers: {}, plot_index: []}\n}\n\n\n function JupyterCommManager() {\n }\n\n JupyterCommManager.prototype.register_target = function(plot_id, comm_id, msg_handler) {\n if (window.comm_manager || ((window.Jupyter !== undefined) && (Jupyter.notebook.kernel != null))) {\n var comm_manager = window.comm_manager || Jupyter.notebook.kernel.comm_manager;\n comm_manager.register_target(comm_id, function(comm) {\n comm.on_msg(msg_handler);\n });\n } else if ((plot_id in window.PyViz.kernels) && (window.PyViz.kernels[plot_id])) {\n window.PyViz.kernels[plot_id].registerCommTarget(comm_id, function(comm) {\n comm.onMsg = msg_handler;\n });\n } else if (typeof google != 'undefined' && google.colab.kernel != null) {\n google.colab.kernel.comms.registerTarget(comm_id, (comm) => {\n var messages = comm.messages[Symbol.asyncIterator]();\n function processIteratorResult(result) {\n var message = result.value;\n console.log(message)\n var content = {data: message.data, comm_id};\n var buffers = []\n for (var buffer of message.buffers || []) {\n buffers.push(new DataView(buffer))\n }\n var metadata = message.metadata || {};\n var msg = {content, buffers, metadata}\n msg_handler(msg);\n return messages.next().then(processIteratorResult);\n }\n return messages.next().then(processIteratorResult);\n })\n }\n }\n\n JupyterCommManager.prototype.get_client_comm = function(plot_id, comm_id, msg_handler) {\n if (comm_id in window.PyViz.comms) {\n return window.PyViz.comms[comm_id];\n } else if (window.comm_manager || ((window.Jupyter !== undefined) && (Jupyter.notebook.kernel != null))) {\n var comm_manager = window.comm_manager || Jupyter.notebook.kernel.comm_manager;\n var comm = comm_manager.new_comm(comm_id, {}, {}, {}, comm_id);\n if (msg_handler) {\n comm.on_msg(msg_handler);\n }\n } else if ((plot_id in window.PyViz.kernels) && (window.PyViz.kernels[plot_id])) {\n var comm = window.PyViz.kernels[plot_id].connectToComm(comm_id);\n comm.open();\n if (msg_handler) {\n comm.onMsg = msg_handler;\n }\n } else if (typeof google != 'undefined' && google.colab.kernel != null) {\n var comm_promise = google.colab.kernel.comms.open(comm_id)\n comm_promise.then((comm) => {\n window.PyViz.comms[comm_id] = comm;\n if (msg_handler) {\n var messages = comm.messages[Symbol.asyncIterator]();\n function processIteratorResult(result) {\n var message = result.value;\n var content = {data: message.data};\n var metadata = message.metadata || {comm_id};\n var msg = {content, metadata}\n msg_handler(msg);\n return messages.next().then(processIteratorResult);\n }\n return messages.next().then(processIteratorResult);\n }\n }) \n var sendClosure = (data, metadata, buffers, disposeOnDone) => {\n return comm_promise.then((comm) => {\n comm.send(data, metadata, buffers, disposeOnDone);\n });\n };\n var comm = {\n send: sendClosure\n };\n }\n window.PyViz.comms[comm_id] = comm;\n return comm;\n }\n window.PyViz.comm_manager = new JupyterCommManager();\n \n\n\nvar JS_MIME_TYPE = 'application/javascript';\nvar HTML_MIME_TYPE = 'text/html';\nvar EXEC_MIME_TYPE = 'application/vnd.holoviews_exec.v0+json';\nvar CLASS_NAME = 'output';\n\n/**\n * Render data to the DOM node\n */\nfunction render(props, node) {\n var div = document.createElement(\"div\");\n var script = document.createElement(\"script\");\n node.appendChild(div);\n node.appendChild(script);\n}\n\n/**\n * Handle when a new output is added\n */\nfunction handle_add_output(event, handle) {\n var output_area = handle.output_area;\n var output = handle.output;\n if ((output.data == undefined) || (!output.data.hasOwnProperty(EXEC_MIME_TYPE))) {\n return\n }\n var id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n var toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n if (id !== undefined) {\n var nchildren = toinsert.length;\n var html_node = toinsert[nchildren-1].children[0];\n html_node.innerHTML = output.data[HTML_MIME_TYPE];\n var scripts = [];\n var nodelist = html_node.querySelectorAll(\"script\");\n for (var i in nodelist) {\n if (nodelist.hasOwnProperty(i)) {\n scripts.push(nodelist[i])\n }\n }\n\n scripts.forEach( function (oldScript) {\n var newScript = document.createElement(\"script\");\n var attrs = [];\n var nodemap = oldScript.attributes;\n for (var j in nodemap) {\n if (nodemap.hasOwnProperty(j)) {\n attrs.push(nodemap[j])\n }\n }\n attrs.forEach(function(attr) { newScript.setAttribute(attr.name, attr.value) });\n newScript.appendChild(document.createTextNode(oldScript.innerHTML));\n oldScript.parentNode.replaceChild(newScript, oldScript);\n });\n if (JS_MIME_TYPE in output.data) {\n toinsert[nchildren-1].children[1].textContent = output.data[JS_MIME_TYPE];\n }\n output_area._hv_plot_id = id;\n if ((window.Bokeh !== undefined) && (id in Bokeh.index)) {\n window.PyViz.plot_index[id] = Bokeh.index[id];\n } else {\n window.PyViz.plot_index[id] = null;\n }\n } else if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n var bk_div = document.createElement(\"div\");\n bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n var script_attrs = bk_div.children[0].attributes;\n for (var i = 0; i < script_attrs.length; i++) {\n toinsert[toinsert.length - 1].childNodes[1].setAttribute(script_attrs[i].name, script_attrs[i].value);\n }\n // store reference to server id on output_area\n output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n }\n}\n\n/**\n * Handle when an output is cleared or removed\n */\nfunction handle_clear_output(event, handle) {\n var id = handle.cell.output_area._hv_plot_id;\n var server_id = handle.cell.output_area._bokeh_server_id;\n if (((id === undefined) || !(id in PyViz.plot_index)) && (server_id !== undefined)) { return; }\n var comm = window.PyViz.comm_manager.get_client_comm(\"hv-extension-comm\", \"hv-extension-comm\", function () {});\n if (server_id !== null) {\n comm.send({event_type: 'server_delete', 'id': server_id});\n return;\n } else if (comm !== null) {\n comm.send({event_type: 'delete', 'id': id});\n }\n delete PyViz.plot_index[id];\n if ((window.Bokeh !== undefined) & (id in window.Bokeh.index)) {\n var doc = window.Bokeh.index[id].model.document\n doc.clear();\n const i = window.Bokeh.documents.indexOf(doc);\n if (i > -1) {\n window.Bokeh.documents.splice(i, 1);\n }\n }\n}\n\n/**\n * Handle kernel restart event\n */\nfunction handle_kernel_cleanup(event, handle) {\n delete PyViz.comms[\"hv-extension-comm\"];\n window.PyViz.plot_index = {}\n}\n\n/**\n * Handle update_display_data messages\n */\nfunction handle_update_output(event, handle) {\n handle_clear_output(event, {cell: {output_area: handle.output_area}})\n handle_add_output(event, handle)\n}\n\nfunction register_renderer(events, OutputArea) {\n function append_mime(data, metadata, element) {\n // create a DOM node to render to\n var toinsert = this.create_output_subarea(\n metadata,\n CLASS_NAME,\n EXEC_MIME_TYPE\n );\n this.keyboard_manager.register_events(toinsert);\n // Render to node\n var props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n render(props, toinsert[0]);\n element.append(toinsert);\n return toinsert\n }\n\n events.on('output_added.OutputArea', handle_add_output);\n events.on('output_updated.OutputArea', handle_update_output);\n events.on('clear_output.CodeCell', handle_clear_output);\n events.on('delete.Cell', handle_clear_output);\n events.on('kernel_ready.Kernel', handle_kernel_cleanup);\n\n OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n safe: true,\n index: 0\n });\n}\n\nif (window.Jupyter !== undefined) {\n try {\n var events = require('base/js/events');\n var OutputArea = require('notebook/js/outputarea').OutputArea;\n if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n register_renderer(events, OutputArea);\n }\n } catch(err) {\n }\n}\n" }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "\n", "
\n", "\n", "\n", "\n", " \n", " \n", "\n", "\n", "\n", "\n", "
\n" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "\n", "
\n", " \n", " Loading BokehJS ...\n", "
\n" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "(function(root) {\n", " function now() {\n", " return new Date();\n", " }\n", "\n", " const force = true;\n", "\n", " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n", " root._bokeh_onload_callbacks = [];\n", " root._bokeh_is_loading = undefined;\n", " }\n", "\n", "const JS_MIME_TYPE = 'application/javascript';\n", " const HTML_MIME_TYPE = 'text/html';\n", " const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", " const CLASS_NAME = 'output_bokeh rendered_html';\n", "\n", " /**\n", " * Render data to the DOM node\n", " */\n", " function render(props, node) {\n", " const script = document.createElement(\"script\");\n", " node.appendChild(script);\n", " }\n", "\n", " /**\n", " * Handle when an output is cleared or removed\n", " */\n", " function handleClearOutput(event, handle) {\n", " const cell = handle.cell;\n", "\n", " const id = cell.output_area._bokeh_element_id;\n", " const server_id = cell.output_area._bokeh_server_id;\n", " // Clean up Bokeh references\n", " if (id != null && id in Bokeh.index) {\n", " Bokeh.index[id].model.document.clear();\n", " delete Bokeh.index[id];\n", " }\n", "\n", " if (server_id !== undefined) {\n", " // Clean up Bokeh references\n", " const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n", " cell.notebook.kernel.execute(cmd_clean, {\n", " iopub: {\n", " output: function(msg) {\n", " const id = msg.content.text.trim();\n", " if (id in Bokeh.index) {\n", " Bokeh.index[id].model.document.clear();\n", " delete Bokeh.index[id];\n", " }\n", " }\n", " }\n", " });\n", " // Destroy server and session\n", " const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", " cell.notebook.kernel.execute(cmd_destroy);\n", " }\n", " }\n", "\n", " /**\n", " * Handle when a new output is added\n", " */\n", " function handleAddOutput(event, handle) {\n", " const output_area = handle.output_area;\n", " const output = handle.output;\n", "\n", " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", " if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n", " return\n", " }\n", "\n", " const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", "\n", " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n", " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n", " // store reference to embed id on output_area\n", " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", " }\n", " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", " const bk_div = document.createElement(\"div\");\n", " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", " const script_attrs = bk_div.children[0].attributes;\n", " for (let i = 0; i < script_attrs.length; i++) {\n", " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n", " toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n", " }\n", " // store reference to server id on output_area\n", " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", " }\n", " }\n", "\n", " function register_renderer(events, OutputArea) {\n", "\n", " function append_mime(data, metadata, element) {\n", " // create a DOM node to render to\n", " const toinsert = this.create_output_subarea(\n", " metadata,\n", " CLASS_NAME,\n", " EXEC_MIME_TYPE\n", " );\n", " this.keyboard_manager.register_events(toinsert);\n", " // Render to node\n", " const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", " render(props, toinsert[toinsert.length - 1]);\n", " element.append(toinsert);\n", " return toinsert\n", " }\n", "\n", " /* Handle when an output is cleared or removed */\n", " events.on('clear_output.CodeCell', handleClearOutput);\n", " events.on('delete.Cell', handleClearOutput);\n", "\n", " /* Handle when a new output is added */\n", " events.on('output_added.OutputArea', handleAddOutput);\n", "\n", " /**\n", " * Register the mime type and append_mime function with output_area\n", " */\n", " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", " /* Is output safe? */\n", " safe: true,\n", " /* Index of renderer in `output_area.display_order` */\n", " index: 0\n", " });\n", " }\n", "\n", " // register the mime type if in Jupyter Notebook environment and previously unregistered\n", " if (root.Jupyter !== undefined) {\n", " const events = require('base/js/events');\n", " const OutputArea = require('notebook/js/outputarea').OutputArea;\n", "\n", " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", " register_renderer(events, OutputArea);\n", " }\n", " }\n", " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n", " root._bokeh_timeout = Date.now() + 5000;\n", " root._bokeh_failed_load = false;\n", " }\n", "\n", " const NB_LOAD_WARNING = {'data': {'text/html':\n", " \"
\\n\"+\n", " \"

\\n\"+\n", " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", " \"

\\n\"+\n", " \"\\n\"+\n", " \"\\n\"+\n", " \"from bokeh.resources import INLINE\\n\"+\n", " \"output_notebook(resources=INLINE)\\n\"+\n", " \"\\n\"+\n", " \"
\"}};\n", "\n", " function display_loaded() {\n", " const el = document.getElementById(\"b6e02f3e-20f9-46d7-9310-988e1b6fef84\");\n", " if (el != null) {\n", " el.textContent = \"BokehJS is loading...\";\n", " }\n", " if (root.Bokeh !== undefined) {\n", " if (el != null) {\n", " el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n", " }\n", " } else if (Date.now() < root._bokeh_timeout) {\n", " setTimeout(display_loaded, 100)\n", " }\n", " }\n", "\n", " function run_callbacks() {\n", " try {\n", " root._bokeh_onload_callbacks.forEach(function(callback) {\n", " if (callback != null)\n", " callback();\n", " });\n", " } finally {\n", " delete root._bokeh_onload_callbacks\n", " }\n", " console.debug(\"Bokeh: all callbacks have finished\");\n", " }\n", "\n", " function load_libs(css_urls, js_urls, callback) {\n", " if (css_urls == null) css_urls = [];\n", " if (js_urls == null) js_urls = [];\n", "\n", " root._bokeh_onload_callbacks.push(callback);\n", " if (root._bokeh_is_loading > 0) {\n", " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", " return null;\n", " }\n", " if (js_urls == null || js_urls.length === 0) {\n", " run_callbacks();\n", " return null;\n", " }\n", " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", " root._bokeh_is_loading = css_urls.length + js_urls.length;\n", "\n", " function on_load() {\n", " root._bokeh_is_loading--;\n", " if (root._bokeh_is_loading === 0) {\n", " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", " run_callbacks()\n", " }\n", " }\n", "\n", " function on_error(url) {\n", " console.error(\"failed to load \" + url);\n", " }\n", "\n", " for (let i = 0; i < css_urls.length; i++) {\n", " const url = css_urls[i];\n", " const element = document.createElement(\"link\");\n", " element.onload = on_load;\n", " element.onerror = on_error.bind(null, url);\n", " element.rel = \"stylesheet\";\n", " element.type = \"text/css\";\n", " element.href = url;\n", " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", " document.body.appendChild(element);\n", " }\n", "\n", " for (let i = 0; i < js_urls.length; i++) {\n", " const url = js_urls[i];\n", " const element = document.createElement('script');\n", " element.onload = on_load;\n", " element.onerror = on_error.bind(null, url);\n", " element.async = false;\n", " element.src = url;\n", " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " document.head.appendChild(element);\n", " }\n", " };\n", "\n", " function inject_raw_css(css) {\n", " const element = document.createElement(\"style\");\n", " element.appendChild(document.createTextNode(css));\n", " document.body.appendChild(element);\n", " }\n", "\n", " const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.1.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.1.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.1.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.1.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.1.1.min.js\", \"https://unpkg.com/@holoviz/panel@1.1.0/dist/panel.min.js\"];\n", " const css_urls = [];\n", "\n", " const inline_js = [ function(Bokeh) {\n", " Bokeh.set_log_level(\"info\");\n", " },\n", "function(Bokeh) {\n", " }\n", " ];\n", "\n", " function run_inline_js() {\n", " if (root.Bokeh !== undefined || force === true) {\n", " for (let i = 0; i < inline_js.length; i++) {\n", " inline_js[i].call(root, root.Bokeh);\n", " }\n", "if (force === true) {\n", " display_loaded();\n", " }} else if (Date.now() < root._bokeh_timeout) {\n", " setTimeout(run_inline_js, 100);\n", " } else if (!root._bokeh_failed_load) {\n", " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", " root._bokeh_failed_load = true;\n", " } else if (force !== true) {\n", " const cell = $(document.getElementById(\"b6e02f3e-20f9-46d7-9310-988e1b6fef84\")).parents('.cell').data().cell;\n", " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", " }\n", " }\n", "\n", " if (root._bokeh_is_loading === 0) {\n", " console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", " run_inline_js();\n", " } else {\n", " load_libs(css_urls, js_urls, function() {\n", " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", " run_inline_js();\n", " });\n", " }\n", "}(window));" ], "application/vnd.bokehjs_load.v0+json": "(function(root) {\n function now() {\n return new Date();\n }\n\n const force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n const NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\"}};\n\n function display_loaded() {\n const el = document.getElementById(\"b6e02f3e-20f9-46d7-9310-988e1b6fef84\");\n if (el != null) {\n el.textContent = \"BokehJS is loading...\";\n }\n if (root.Bokeh !== undefined) {\n if (el != null) {\n el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(display_loaded, 100)\n }\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n\n function on_error(url) {\n console.error(\"failed to load \" + url);\n }\n\n for (let i = 0; i < css_urls.length; i++) {\n const url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n }\n\n for (let i = 0; i < js_urls.length; i++) {\n const url = js_urls[i];\n const element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.1.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.1.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.1.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.1.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.1.1.min.js\", \"https://unpkg.com/@holoviz/panel@1.1.0/dist/panel.min.js\"];\n const css_urls = [];\n\n const inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {\n }\n ];\n\n function run_inline_js() {\n if (root.Bokeh !== undefined || force === true) {\n for (let i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\nif (force === true) {\n display_loaded();\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n } else if (force !== true) {\n const cell = $(document.getElementById(\"b6e02f3e-20f9-46d7-9310-988e1b6fef84\")).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\n }\n\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n run_inline_js();\n } else {\n load_libs(css_urls, js_urls, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));" }, "metadata": {}, "output_type": "display_data" } ], "source": [ "import os\n", "import glob\n", "\n", "import numpy as np\n", "import pandas as pd\n", "\n", "import skimage.io\n", "import skimage.morphology\n", "import skimage.segmentation\n", "import skimage.measure\n", "\n", "import iqplot\n", "\n", "import holoviews as hv\n", "hv.extension('bokeh')\n", "\n", "import bokeh.io\n", "bokeh.io.output_notebook()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "
\n", "\n", "We already wrote cell segmentation functions in [Exercise 6.2](exercise_6.2_solution.ipynb). The call signature is\n", "\n", "```python\n", "cell_segmenter(im, thresh='otsu', radius=20.0, image_mode='phase',\n", " area_bounds=(0, 1e7), ecc_bounds=(0, 1))\n", "```\n", " \n", "We will include that code here so it is available. In practice, you would have this code in a module that you would have installed on your machine. " ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "def cell_segmenter(\n", " im,\n", " thresh=\"otsu\",\n", " radius=20.0,\n", " image_mode=\"phase\",\n", " area_bounds=(0, 1e7),\n", " ecc_bounds=(0, 1),\n", "):\n", " \"\"\"\n", " This function segments a given image via thresholding and returns\n", " a labeled segmentation mask.\n", " \n", " Parameters\n", " ----------\n", " im : 2d-array\n", " Image to be segmented. This may be of either float or integer\n", " data type.\n", " thresh : int, float, or 'otsu'\n", " Value used during thresholding operation. This can either be a value \n", " (`int` or `float`) or 'otsu'. If 'otsu', the threshold value will be \n", " determined automatically using Otsu's thresholding method.\n", " radius : float\n", " Radius for gaussian blur for background subtraction. Default value\n", " is 20.\n", " image_mode : 'phase' or 'fluorescence'\n", " Mode of microscopy used to capture the image. If 'phase', objects with \n", " intensity values *lower* than the provided threshold will be selected. \n", " If `fluorescence`, values *greater* than the provided threshold will be \n", " selected. Default value is 'phase'.\n", " area_bounds : tuple of ints.\n", " Range of areas of acceptable objects. This should be provided in units \n", " of square pixels.\n", " ecc_bounds : tuple of floats\n", " Range of eccentricity values of acceptable objects. These values should\n", " range between 0.0 and 1.0.\n", " \n", " Returns\n", " -------\n", " im_labeled : 2d-array, int\n", " Labeled segmentation mask.\n", " \"\"\"\n", " # Apply a median filter to remove hot pixels.\n", " med_selem = skimage.morphology.square(3)\n", " im_filt = skimage.filters.median(im, footprint=med_selem)\n", "\n", " # Perform gaussian subtraction\n", " im_sub = bg_subtract(im_filt, radius)\n", "\n", " # Determine the thresholding method.\n", " if thresh == \"otsu\":\n", " thresh = skimage.filters.threshold_otsu(im_sub)\n", "\n", " # Determine the image mode and apply threshold.\n", " if image_mode == \"phase\":\n", " im_thresh = im_sub < thresh\n", " elif image_mode == \"fluorescence\":\n", " im_thresh = im_sub > thresh\n", " else:\n", " raise ValueError(\n", " \"image mode not recognized. Must be 'phase'\" + \" or 'fluorescence'\"\n", " )\n", "\n", " # Label the objects.\n", " im_label = skimage.measure.label(im_thresh)\n", "\n", " # Apply the area and eccentricity bounds.\n", " im_filt = area_ecc_filter(im_label, area_bounds, ecc_bounds)\n", "\n", " # Remove objects touching the border.\n", " im_border = skimage.segmentation.clear_border(im_filt, buffer_size=5)\n", "\n", " # Relabel the image.\n", " im_border = im_border > 0\n", "\n", " return skimage.measure.label(im_border)\n", "\n", "\n", "def bg_subtract(im, radius):\n", " \"\"\"\n", " Subtracts a gaussian blurred image from itself smoothing uneven \n", " illumination.\n", " \n", " Parameters\n", " ----------\n", " im : 2d-array\n", " Image to be subtracted\n", " radius : int or float\n", " Radius of gaussian blur\n", " \n", " Returns\n", " -------\n", " im_sub : 2d-array, float\n", " Background subtracted image.\n", " \"\"\"\n", " # Apply the gaussian filter.\n", " im_filt = skimage.filters.gaussian(im, radius)\n", "\n", " # Ensure the original image is a float\n", " if np.max(im) > 1.0:\n", " im = skimage.img_as_float(im)\n", "\n", " return im - im_filt\n", "\n", "\n", "def area_ecc_filter(im, area_bounds, ecc_bounds):\n", " \"\"\"\n", " Filters objects in an image based on their areas.\n", " \n", " Parameters\n", " ----------\n", " im : 2d-array, int\n", " Labeled segmentation mask to be filtered. \n", " area_bounds : tuple of ints\n", " Range of areas in which acceptable objects exist. This should be \n", " provided in units of square pixels.\n", " ecc_bounds : tuple of floats \n", " Range of eccentricities in which acceptable objects exist. This should be \n", " provided on the range of 0 to 1.0.\n", " \n", " Returns\n", " -------\n", " im_relab : 2d-array, int\n", " The relabeled, filtered image.\n", " \"\"\"\n", "\n", " # Extract the region props of the objects.\n", " props = skimage.measure.regionprops(im)\n", "\n", " # Extract the areas and labels.\n", " areas = np.array([prop.area for prop in props])\n", " eccs = np.array([prop.eccentricity for prop in props])\n", " labels = np.array([prop.label for prop in props])\n", "\n", " # Make an empty image to add the approved cells.\n", " im_approved = np.zeros_like(im)\n", "\n", " # Threshold the objects based on area and eccentricity\n", " for i, _ in enumerate(areas):\n", " if (\n", " areas[i] > area_bounds[0]\n", " and areas[i] < area_bounds[1]\n", " and eccs[i] > ecc_bounds[0]\n", " and eccs[i] < ecc_bounds[1]\n", " ):\n", " im_approved += im == labels[i]\n", "\n", " # Relabel the image.\n", " return skimage.measure.label(im_approved > 0)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Now we need to figure out some way in which we can iterate over all of our images in `data/HG105_images`. We have a few options here. First, and this is the worst solution, we could type out the name of each individual file and load them individually. The other option (a better option) is to make our computer get the list of all files in a single (or a few) lines of code. To do this, we will use the `glob` module. `glob` has a bunch of methods for obtaining filenames from directories. The most useful method of `glob` is `glob` which will return a list of paths that match a given pattern. Let's see how well it works for our needs. " ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "['data/HG105_images/noLac_phase_0000.tif', 'data/HG105_images/noLac_phase_0001.tif', 'data/HG105_images/noLac_phase_0002.tif', 'data/HG105_images/noLac_phase_0003.tif', 'data/HG105_images/noLac_phase_0004.tif', 'data/HG105_images/noLac_phase_0005.tif', 'data/HG105_images/noLac_phase_0006.tif', 'data/HG105_images/noLac_phase_0007.tif', 'data/HG105_images/noLac_phase_0008.tif']\n", "['data/HG105_images/noLac_FITC_0000.tif', 'data/HG105_images/noLac_FITC_0001.tif', 'data/HG105_images/noLac_FITC_0002.tif', 'data/HG105_images/noLac_FITC_0003.tif', 'data/HG105_images/noLac_FITC_0004.tif', 'data/HG105_images/noLac_FITC_0005.tif', 'data/HG105_images/noLac_FITC_0006.tif', 'data/HG105_images/noLac_FITC_0007.tif', 'data/HG105_images/noLac_FITC_0008.tif']\n" ] } ], "source": [ "# Glob the phase and fluo globs. \n", "phase_glob = list(sorted(glob.glob('data/HG105_images/*phase*.tif')))\n", "fluo_glob = list(sorted(glob.glob('data/HG105_images/*FITC*.tif')))\n", "\n", "# Take a look.\n", "print(phase_glob)\n", "print(fluo_glob)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Well, that was easy. We used the wildcard character (`*`) to find all files that had the pattern `anything` then the strings `phase` or `FITC` followed by *anything* so long that it had a `.tif` extension. The output is a little bit different as well in that it not only returned the name of the file in the specified `data_dir`, but it gave us the entire relative path. This is an important distinction and is actually one of the reasons I frequently use `glob.glob`.\n", "\n", "Now that we have a list of files, we should iterate over each phase image, perform the segmentation, then extract the mean pixel intensities of each object and store them in a list." ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [], "source": [ "# Instantiate an empty list for the mean pixel intensity of each cell.\n", "mean_ints = []\n", "\n", "# Do the same for the areas.\n", "areas = []\n", "\n", "# Image index\n", "image_numbers = []\n", "\n", "# Define our area and eccentricity bounds for the segmentation function.\n", "ip_dist = 0.0626 # in units of µm per pixel\n", "area_bounds = (0.5 / ip_dist ** 2, 4 / ip_dist ** 2)\n", "ecc_bounds = (0.8, 1.0)\n", "\n", "# Loop through all images.\n", "for i, pf in enumerate(zip(phase_glob, fluo_glob)):\n", " p, f = pf\n", " # Load the phase image.\n", " phase_im = skimage.io.imread(p)\n", "\n", " # Perform the segmentation.\n", " phase_seg = cell_segmenter(\n", " phase_im,\n", " image_mode=\"phase\",\n", " area_bounds=area_bounds,\n", " ecc_bounds=ecc_bounds,\n", " )\n", "\n", " # Load the fluorescence image.\n", " fluo_im = skimage.io.imread(f)\n", "\n", " # Compute the region properties.\n", " props = skimage.measure.regionprops(phase_seg, intensity_image=fluo_im)\n", "\n", " # Add them to our storage lists.\n", " for prop in props:\n", " mean_ints.append(prop.mean_intensity)\n", " areas.append(prop.area * ip_dist ** 2)\n", " image_numbers.append(i)\n", "\n", "# Units don't matter, so normalize integrated intensity\n", "mean_ints = np.array(mean_ints)\n", "mean_ints /= mean_ints.max()\n", "\n", "# Store results in data frame\n", "df = pd.DataFrame(\n", " {\n", " \"mean intensity\": mean_ints / max(mean_ints),\n", " \"area\": areas,\n", " \"image number\": image_numbers,\n", " }\n", ")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "So, in just a few seconds, were were able to do what would take hours (if not a full day) to do in ImageJ by clicking. To make sure things are working as expected, let's take a look at the last segmentation mask generated. We can use the `make_overlay()` function from [Exercise 10.2](exercise_10.2_solution.ipynb). Remember that the array `phase_seg` is the labeled image, so to get the binary image, we use `phase_seg > 0`." ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "data": {}, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.holoviews_exec.v0+json": "", "text/html": [ "
\n", "
\n", "
\n", "" ], "text/plain": [ ":RGB [x,y] (R,G,B)" ] }, "execution_count": 5, "metadata": { "application/vnd.holoviews_exec.v0+json": { "id": "p1002" } }, "output_type": "execute_result" } ], "source": [ "def make_overlay(im, im_bw):\n", " \"\"\"Create RGB image with cyan channel saturated via segmentation mask.\"\"\"\n", " # Make float and normalized image\n", " im = np.copy(im).astype(float)\n", "\n", " # Build RGB image by stacking grayscale images\n", " im_rgb = np.dstack(3 * [im / im.max()])\n", "\n", " # Saturate cyan channel wherever there are white pixels in thresh image\n", " im_rgb[im_bw, 0] = 1.0\n", "\n", " return im_rgb\n", "\n", "\n", "im_rgb = make_overlay(phase_im, phase_seg > 0)\n", "\n", "hv.RGB(im_rgb).opts(\n", " frame_width=300, frame_height=phase_im.shape[0] * 300 // phase_im.shape[0]\n", ")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "That looks pretty great to me, let's see how many cells we were actually able to measure. " ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Segmented and analyzed 92 cells!\n" ] } ], "source": [ "# Print the total number of cells. \n", "print(\"Segmented and analyzed {num} cells!\".format(num=len(df)))" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Analyzing 92 cells in only 8 images in about 8 seconds is actually pretty good! That's certainly enough to do some serious boot strapping. Let's look at the ECDFs of the mean intensities and the areas. " ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
\n" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "(function(root) {\n", " function embed_document(root) {\n", " const docs_json = {\"8a94197d-836c-44cc-9618-8f6d7bf12ffe\":{\"version\":\"3.1.1\",\"title\":\"Bokeh Application\",\"defs\":[{\"type\":\"model\",\"name\":\"ReactiveHTML1\"},{\"type\":\"model\",\"name\":\"FlexBox1\",\"properties\":[{\"name\":\"align_content\",\"kind\":\"Any\",\"default\":\"flex-start\"},{\"name\":\"align_items\",\"kind\":\"Any\",\"default\":\"flex-start\"},{\"name\":\"flex_direction\",\"kind\":\"Any\",\"default\":\"row\"},{\"name\":\"flex_wrap\",\"kind\":\"Any\",\"default\":\"wrap\"},{\"name\":\"justify_content\",\"kind\":\"Any\",\"default\":\"flex-start\"}]},{\"type\":\"model\",\"name\":\"FloatPanel1\",\"properties\":[{\"name\":\"config\",\"kind\":\"Any\",\"default\":{\"type\":\"map\"}},{\"name\":\"contained\",\"kind\":\"Any\",\"default\":true},{\"name\":\"position\",\"kind\":\"Any\",\"default\":\"right-top\"},{\"name\":\"offsetx\",\"kind\":\"Any\",\"default\":null},{\"name\":\"offsety\",\"kind\":\"Any\",\"default\":null},{\"name\":\"theme\",\"kind\":\"Any\",\"default\":\"primary\"},{\"name\":\"status\",\"kind\":\"Any\",\"default\":\"normalized\"}]},{\"type\":\"model\",\"name\":\"GridStack1\",\"properties\":[{\"name\":\"mode\",\"kind\":\"Any\",\"default\":\"warn\"},{\"name\":\"ncols\",\"kind\":\"Any\",\"default\":null},{\"name\":\"nrows\",\"kind\":\"Any\",\"default\":null},{\"name\":\"allow_resize\",\"kind\":\"Any\",\"default\":true},{\"name\":\"allow_drag\",\"kind\":\"Any\",\"default\":true},{\"name\":\"state\",\"kind\":\"Any\",\"default\":[]}]},{\"type\":\"model\",\"name\":\"drag1\",\"properties\":[{\"name\":\"slider_width\",\"kind\":\"Any\",\"default\":5},{\"name\":\"slider_color\",\"kind\":\"Any\",\"default\":\"black\"},{\"name\":\"value\",\"kind\":\"Any\",\"default\":50}]},{\"type\":\"model\",\"name\":\"click1\",\"properties\":[{\"name\":\"terminal_output\",\"kind\":\"Any\",\"default\":\"\"},{\"name\":\"debug_name\",\"kind\":\"Any\",\"default\":\"\"},{\"name\":\"clears\",\"kind\":\"Any\",\"default\":0}]},{\"type\":\"model\",\"name\":\"FastWrapper1\",\"properties\":[{\"name\":\"object\",\"kind\":\"Any\",\"default\":null},{\"name\":\"style\",\"kind\":\"Any\",\"default\":null}]},{\"type\":\"model\",\"name\":\"NotificationAreaBase1\",\"properties\":[{\"name\":\"position\",\"kind\":\"Any\",\"default\":\"bottom-right\"},{\"name\":\"_clear\",\"kind\":\"Any\",\"default\":0}]},{\"type\":\"model\",\"name\":\"NotificationArea1\",\"properties\":[{\"name\":\"notifications\",\"kind\":\"Any\",\"default\":[]},{\"name\":\"position\",\"kind\":\"Any\",\"default\":\"bottom-right\"},{\"name\":\"_clear\",\"kind\":\"Any\",\"default\":0},{\"name\":\"types\",\"kind\":\"Any\",\"default\":[{\"type\":\"map\",\"entries\":[[\"type\",\"warning\"],[\"background\",\"#ffc107\"],[\"icon\",{\"type\":\"map\",\"entries\":[[\"className\",\"fas fa-exclamation-triangle\"],[\"tagName\",\"i\"],[\"color\",\"white\"]]}]]},{\"type\":\"map\",\"entries\":[[\"type\",\"info\"],[\"background\",\"#007bff\"],[\"icon\",{\"type\":\"map\",\"entries\":[[\"className\",\"fas fa-info-circle\"],[\"tagName\",\"i\"],[\"color\",\"white\"]]}]]}]}]},{\"type\":\"model\",\"name\":\"Notification\",\"properties\":[{\"name\":\"background\",\"kind\":\"Any\",\"default\":null},{\"name\":\"duration\",\"kind\":\"Any\",\"default\":3000},{\"name\":\"icon\",\"kind\":\"Any\",\"default\":null},{\"name\":\"message\",\"kind\":\"Any\",\"default\":\"\"},{\"name\":\"notification_type\",\"kind\":\"Any\",\"default\":null},{\"name\":\"_destroyed\",\"kind\":\"Any\",\"default\":false}]},{\"type\":\"model\",\"name\":\"TemplateActions1\",\"properties\":[{\"name\":\"open_modal\",\"kind\":\"Any\",\"default\":0},{\"name\":\"close_modal\",\"kind\":\"Any\",\"default\":0}]},{\"type\":\"model\",\"name\":\"BootstrapTemplateActions1\",\"properties\":[{\"name\":\"open_modal\",\"kind\":\"Any\",\"default\":0},{\"name\":\"close_modal\",\"kind\":\"Any\",\"default\":0}]},{\"type\":\"model\",\"name\":\"MaterialTemplateActions1\",\"properties\":[{\"name\":\"open_modal\",\"kind\":\"Any\",\"default\":0},{\"name\":\"close_modal\",\"kind\":\"Any\",\"default\":0}]}],\"roots\":[{\"type\":\"object\",\"name\":\"Row\",\"id\":\"p1281\",\"attributes\":{\"children\":[{\"type\":\"object\",\"name\":\"Figure\",\"id\":\"p1147\",\"attributes\":{\"width\":300,\"height\":200,\"x_range\":{\"type\":\"object\",\"name\":\"DataRange1d\",\"id\":\"p1149\"},\"y_range\":{\"type\":\"object\",\"name\":\"DataRange1d\",\"id\":\"p1148\"},\"x_scale\":{\"type\":\"object\",\"name\":\"LinearScale\",\"id\":\"p1160\"},\"y_scale\":{\"type\":\"object\",\"name\":\"LinearScale\",\"id\":\"p1162\"},\"title\":{\"type\":\"object\",\"name\":\"Title\",\"id\":\"p1151\"},\"renderers\":[{\"type\":\"object\",\"name\":\"GlyphRenderer\",\"id\":\"p1199\",\"attributes\":{\"data_source\":{\"type\":\"object\",\"name\":\"ColumnDataSource\",\"id\":\"p1193\",\"attributes\":{\"selected\":{\"type\":\"object\",\"name\":\"Selection\",\"id\":\"p1195\",\"attributes\":{\"indices\":[],\"line_indices\":[]}},\"selection_policy\":{\"type\":\"object\",\"name\":\"UnionRenderers\",\"id\":\"p1194\"},\"data\":{\"type\":\"map\",\"entries\":[[\"x\",[0.19695954182335965,0.19695954182335965,0.19695954182335965,0.19695954182335965,0.19695954182335965,0.19695954182335965,0.19833082198173688,0.19833082198173688,0.19833082198173688,0.19833082198173688,0.2046431300801895,0.2046431300801895,0.2046431300801895,0.2046431300801895,0.2064083505673126,0.2064083505673126,0.32345153542887695,0.32345153542887695,0.32345153542887695,0.32345153542887695,0.3273086660381438,0.3273086660381438,0.3313052415170778,0.3313052415170778,0.331885118712312,0.331885118712312,0.331885118712312,0.331885118712312,0.3326365637766327,0.3326365637766327,0.3361336650067982,0.3361336650067982,0.339148042999463,0.339148042999463,0.34228256816006486,0.34228256816006486,0.3470495356477451,0.3470495356477451,0.3470495356477451,0.3470495356477451,0.3472402857948521,0.3472402857948521,0.35105503327342097,0.35105503327342097,0.3511848253441219,0.3511848253441219,0.3515710208555537,0.3515710208555537,0.3522070440136437,0.3522070440136437,0.3522070440136437,0.3522070440136437,0.35527625126375306,0.35527625126375306,0.3554954362745018,0.3554954362745018,0.35709123347422933,0.35709123347422933,0.35988407507203635,0.35988407507203635,0.3618887942315418,0.3618887942315418,0.3634793240894384,0.3634793240894384,0.3647250345182253,0.3647250345182253,0.3652104573263374,0.3652104573263374,0.3652104573263374,0.3652104573263374,0.36567949233575375,0.36567949233575375,0.3675249090415697,0.3675249090415697,0.36776415261550965,0.36776415261550965,0.36903022695476945,0.36903022695476945,0.36935430754751924,0.36935430754751924,0.37051476282750456,0.37051476282750456,0.3706865791154505,0.3706865791154505,0.3712188508565844,0.3712188508565844,0.3712609318088679,0.3712609318088679,0.3713404790195607,0.3713404790195607,0.3731311019163704,0.3731311019163704,0.37445600438966453,0.37445600438966453,0.37493429778213316,0.37493429778213316,0.37610639128767603,0.37610639128767603,0.37610639128767603,0.37610639128767603,0.3793256867915689,0.3793256867915689,0.3800331789510937,0.3800331789510937,0.3812246602104803,0.3812246602104803,0.38265510053302254,0.38265510053302254,0.38433438812158666,0.38433438812158666,0.3871280402643846,0.3871280402643846,0.38785874472299275,0.38785874472299275,0.38820700706711775,0.38820700706711775,0.38832645196553817,0.38832645196553817,0.3898053459350577,0.3898053459350577,0.38994693492119853,0.38994693492119853,0.39020965385960954,0.39020965385960954,0.3907618067354765,0.3907618067354765,0.39332727210659724,0.39332727210659724,0.39461283205424974,0.39461283205424974,0.39653780577696657,0.39653780577696657,0.39762545347739664,0.39762545347739664,0.39825913648373507,0.39825913648373507,0.4006393176490408,0.4006393176490408,0.4010410367403065,0.4010410367403065,0.40120780532946165,0.40120780532946165,0.40399813318729727,0.40399813318729727,0.4099495128418767,0.4099495128418767,0.41223193716122125,0.41223193716122125,0.41334077295422894,0.41334077295422894,0.4164969745633456,0.4164969745633456,0.4174489752247901,0.4174489752247901,0.41918009319961963,0.41918009319961963,0.4216989632092744,0.4216989632092744,0.4233894557342902,0.4233894557342902,0.42430357064583324,0.42430357064583324,0.42932871520477994,0.42932871520477994,0.4294728170018444,0.4294728170018444,0.43719058463278004,0.43719058463278004,0.4420603084030383,0.4420603084030383,0.44967392397684486,0.44967392397684486,0.4515520134211287,0.4515520134211287,0.4636796544979722,0.4636796544979722,0.4757265313229039,0.4757265313229039,0.49767531812346183,0.49767531812346183,0.518476643181485,0.518476643181485,0.5519139545380288,0.5519139545380288,1.0,1.0,1.0,1.0,1.0,1.0,0.8322349523454232,0.8322349523454232,0.8322349523454232,0.8322349523454232,0.6262794891016886,0.6262794891016886,0.6262794891016886,0.6262794891016886,0.5519139545380288,0.5519139545380288,0.5492719371225324,0.5492719371225324,0.5492719371225324,0.5492719371225324,0.518476643181485,0.518476643181485,0.5154898837515246,0.5154898837515246,0.49767531812346183,0.49767531812346183,0.49767531812346183,0.49767531812346183,0.4757265313229039,0.4757265313229039,0.4636796544979722,0.4636796544979722,0.45720618589747025,0.45720618589747025,0.45720618589747025,0.45720618589747025,0.4515520134211287,0.4515520134211287,0.44967392397684486,0.44967392397684486,0.4420603084030383,0.4420603084030383,0.44186979551247263,0.44186979551247263,0.43719058463278004,0.43719058463278004,0.4294728170018444,0.4294728170018444,0.4294728170018444,0.4294728170018444,0.42932871520477994,0.42932871520477994,0.42430357064583324,0.42430357064583324,0.4233894557342902,0.4233894557342902,0.4228141679320019,0.4228141679320019,0.4216989632092744,0.4216989632092744,0.41918009319961963,0.41918009319961963,0.4174489752247901,0.4174489752247901,0.4165207745798814,0.4165207745798814,0.41334077295422894,0.41334077295422894,0.41223193716122125,0.41223193716122125,0.41223193716122125,0.41223193716122125,0.4099495128418767,0.4099495128418767,0.40399813318729727,0.40399813318729727,0.4019719135385752,0.4019719135385752,0.40120780532946165,0.40120780532946165,0.4010410367403065,0.4010410367403065,0.4006393176490408,0.4006393176490408,0.39825913648373507,0.39825913648373507,0.39762545347739664,0.39762545347739664,0.39653780577696657,0.39653780577696657,0.39461283205424974,0.39461283205424974,0.39332727210659724,0.39332727210659724,0.3907618067354765,0.3907618067354765,0.39020965385960954,0.39020965385960954,0.38994693492119853,0.38994693492119853,0.3898053459350577,0.3898053459350577,0.38832645196553817,0.38832645196553817,0.38820700706711775,0.38820700706711775,0.38785874472299275,0.38785874472299275,0.3871280402643846,0.3871280402643846,0.3850636751059863,0.3850636751059863,0.38433438812158666,0.38433438812158666,0.38265510053302254,0.38265510053302254,0.3812246602104803,0.3812246602104803,0.3800331789510937,0.3800331789510937,0.3793256867915689,0.3793256867915689,0.37610639128767603,0.37610639128767603,0.37493429778213316,0.37493429778213316,0.37445600438966453,0.37445600438966453,0.3731311019163704,0.3731311019163704,0.3713404790195607,0.3713404790195607,0.3712609318088679,0.3712609318088679,0.3712188508565844,0.3712188508565844,0.3706865791154505,0.3706865791154505,0.37051476282750456,0.37051476282750456,0.36935430754751924,0.36935430754751924,0.36776415261550965,0.36776415261550965,0.3675249090415697,0.3675249090415697,0.36567949233575375,0.36567949233575375,0.3652104573263374,0.3652104573263374,0.3647250345182253,0.3647250345182253,0.3634793240894384,0.3634793240894384,0.3618887942315418,0.3618887942315418,0.35709123347422933,0.35709123347422933,0.3554954362745018,0.3554954362745018,0.35527625126375306,0.35527625126375306,0.3522070440136437,0.3522070440136437,0.3515710208555537,0.3515710208555537,0.3511848253441219,0.3511848253441219,0.3472402857948521,0.3472402857948521,0.3470495356477451,0.3470495356477451,0.34228256816006486,0.34228256816006486,0.339148042999463,0.339148042999463,0.3326365637766327,0.3326365637766327,0.331885118712312,0.331885118712312,0.3273086660381438,0.3273086660381438,0.2064083505673126,0.2064083505673126]],[\"y\",[0.0,0.010869565217391304,0.010869565217391304,0.021739130434782608,0.021739130434782608,0.03260869565217391,0.03260869565217391,0.043478260869565216,0.043478260869565216,0.05434782608695652,0.05434782608695652,0.06521739130434782,0.06521739130434782,0.07608695652173914,0.07608695652173914,0.08695652173913043,0.08695652173913043,0.09782608695652174,0.09782608695652174,0.10869565217391304,0.10869565217391304,0.11956521739130435,0.11956521739130435,0.13043478260869565,0.13043478260869565,0.14130434782608695,0.14130434782608695,0.15217391304347827,0.15217391304347827,0.16304347826086957,0.16304347826086957,0.17391304347826086,0.17391304347826086,0.18478260869565216,0.18478260869565216,0.1956521739130435,0.1956521739130435,0.20652173913043478,0.20652173913043478,0.21739130434782608,0.21739130434782608,0.22826086956521738,0.22826086956521738,0.2391304347826087,0.2391304347826087,0.25,0.25,0.2608695652173913,0.2608695652173913,0.2717391304347826,0.2717391304347826,0.2826086956521739,0.2826086956521739,0.29347826086956524,0.29347826086956524,0.30434782608695654,0.30434782608695654,0.31521739130434784,0.31521739130434784,0.32608695652173914,0.32608695652173914,0.33695652173913043,0.33695652173913043,0.34782608695652173,0.34782608695652173,0.358695652173913,0.358695652173913,0.3695652173913043,0.3695652173913043,0.3804347826086957,0.3804347826086957,0.391304347826087,0.391304347826087,0.40217391304347827,0.40217391304347827,0.41304347826086957,0.41304347826086957,0.42391304347826086,0.42391304347826086,0.43478260869565216,0.43478260869565216,0.44565217391304346,0.44565217391304346,0.45652173913043476,0.45652173913043476,0.4673913043478261,0.4673913043478261,0.4782608695652174,0.4782608695652174,0.4891304347826087,0.4891304347826087,0.5,0.5,0.5108695652173914,0.5108695652173914,0.5217391304347826,0.5217391304347826,0.532608695652174,0.532608695652174,0.5434782608695652,0.5434782608695652,0.5543478260869565,0.5543478260869565,0.5652173913043478,0.5652173913043478,0.5760869565217391,0.5760869565217391,0.5869565217391305,0.5869565217391305,0.5978260869565217,0.5978260869565217,0.6086956521739131,0.6086956521739131,0.6195652173913043,0.6195652173913043,0.6304347826086957,0.6304347826086957,0.6413043478260869,0.6413043478260869,0.6521739130434783,0.6521739130434783,0.6630434782608695,0.6630434782608695,0.6739130434782609,0.6739130434782609,0.6847826086956522,0.6847826086956522,0.6956521739130435,0.6956521739130435,0.7065217391304348,0.7065217391304348,0.717391304347826,0.717391304347826,0.7282608695652174,0.7282608695652174,0.7391304347826086,0.7391304347826086,0.75,0.75,0.7608695652173914,0.7608695652173914,0.7717391304347826,0.7717391304347826,0.782608695652174,0.782608695652174,0.7934782608695652,0.7934782608695652,0.8043478260869565,0.8043478260869565,0.8152173913043478,0.8152173913043478,0.8260869565217391,0.8260869565217391,0.8369565217391305,0.8369565217391305,0.8478260869565217,0.8478260869565217,0.8586956521739131,0.8586956521739131,0.8695652173913043,0.8695652173913043,0.8804347826086957,0.8804347826086957,0.8913043478260869,0.8913043478260869,0.9021739130434783,0.9021739130434783,0.9130434782608695,0.9130434782608695,0.9239130434782609,0.9239130434782609,0.9347826086956522,0.9347826086956522,0.9456521739130435,0.9456521739130435,0.9565217391304348,0.9565217391304348,0.967391304347826,0.967391304347826,0.9782608695652174,0.9782608695652174,0.9891304347826086,0.9891304347826086,1.0,1.0,0.9891304347826086,0.9891304347826086,0.9782608695652174,0.9782608695652174,0.967391304347826,0.967391304347826,0.9565217391304348,0.9565217391304348,0.9456521739130435,0.9456521739130435,0.9347826086956522,0.9347826086956522,0.9239130434782609,0.9239130434782609,0.9130434782608695,0.9130434782608695,0.9021739130434783,0.9021739130434783,0.8913043478260869,0.8913043478260869,0.8804347826086957,0.8804347826086957,0.8695652173913043,0.8695652173913043,0.8586956521739131,0.8586956521739131,0.8478260869565217,0.8478260869565217,0.8369565217391305,0.8369565217391305,0.8260869565217391,0.8260869565217391,0.8152173913043478,0.8152173913043478,0.8043478260869565,0.8043478260869565,0.7934782608695652,0.7934782608695652,0.782608695652174,0.782608695652174,0.7717391304347826,0.7717391304347826,0.7608695652173914,0.7608695652173914,0.75,0.75,0.7391304347826086,0.7391304347826086,0.7282608695652174,0.7282608695652174,0.717391304347826,0.717391304347826,0.7065217391304348,0.7065217391304348,0.6956521739130435,0.6956521739130435,0.6847826086956522,0.6847826086956522,0.6739130434782609,0.6739130434782609,0.6630434782608695,0.6630434782608695,0.6521739130434783,0.6521739130434783,0.6413043478260869,0.6413043478260869,0.6304347826086957,0.6304347826086957,0.6195652173913043,0.6195652173913043,0.6086956521739131,0.6086956521739131,0.5978260869565217,0.5978260869565217,0.5869565217391305,0.5869565217391305,0.5760869565217391,0.5760869565217391,0.5652173913043478,0.5652173913043478,0.5543478260869565,0.5543478260869565,0.5434782608695652,0.5434782608695652,0.532608695652174,0.532608695652174,0.5217391304347826,0.5217391304347826,0.5108695652173914,0.5108695652173914,0.5,0.5,0.4891304347826087,0.4891304347826087,0.4782608695652174,0.4782608695652174,0.4673913043478261,0.4673913043478261,0.45652173913043476,0.45652173913043476,0.44565217391304346,0.44565217391304346,0.43478260869565216,0.43478260869565216,0.42391304347826086,0.42391304347826086,0.41304347826086957,0.41304347826086957,0.40217391304347827,0.40217391304347827,0.391304347826087,0.391304347826087,0.3804347826086957,0.3804347826086957,0.3695652173913043,0.3695652173913043,0.358695652173913,0.358695652173913,0.34782608695652173,0.34782608695652173,0.33695652173913043,0.33695652173913043,0.32608695652173914,0.32608695652173914,0.31521739130434784,0.31521739130434784,0.30434782608695654,0.30434782608695654,0.29347826086956524,0.29347826086956524,0.2826086956521739,0.2826086956521739,0.2717391304347826,0.2717391304347826,0.2608695652173913,0.2608695652173913,0.25,0.25,0.2391304347826087,0.2391304347826087,0.22826086956521738,0.22826086956521738,0.21739130434782608,0.21739130434782608,0.20652173913043478,0.20652173913043478,0.1956521739130435,0.1956521739130435,0.18478260869565216,0.18478260869565216,0.17391304347826086,0.17391304347826086,0.16304347826086957,0.16304347826086957,0.15217391304347827,0.15217391304347827,0.14130434782608695,0.14130434782608695,0.13043478260869565,0.13043478260869565,0.11956521739130435,0.11956521739130435,0.10869565217391304,0.10869565217391304,0.09782608695652174,0.09782608695652174,0.08695652173913043,0.08695652173913043,0.07608695652173914,0.07608695652173914,0.06521739130434782,0.06521739130434782,0.05434782608695652,0.05434782608695652,0.043478260869565216,0.043478260869565216,0.03260869565217391,0.03260869565217391,0.021739130434782608,0.021739130434782608,0.010869565217391304,0.010869565217391304,0.0]]]}}},\"view\":{\"type\":\"object\",\"name\":\"CDSView\",\"id\":\"p1200\",\"attributes\":{\"filter\":{\"type\":\"object\",\"name\":\"AllIndices\",\"id\":\"p1201\"}}},\"glyph\":{\"type\":\"object\",\"name\":\"Patch\",\"id\":\"p1196\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"x\"},\"y\":{\"type\":\"field\",\"field\":\"y\"},\"line_color\":\"#1f77b4\",\"line_alpha\":0,\"fill_color\":\"#1f77b3\",\"fill_alpha\":0.3}},\"nonselection_glyph\":{\"type\":\"object\",\"name\":\"Patch\",\"id\":\"p1197\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"x\"},\"y\":{\"type\":\"field\",\"field\":\"y\"},\"line_color\":\"#1f77b4\",\"line_alpha\":0.1,\"fill_color\":\"#1f77b3\",\"fill_alpha\":0.1,\"hatch_alpha\":0.1}},\"muted_glyph\":{\"type\":\"object\",\"name\":\"Patch\",\"id\":\"p1198\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"x\"},\"y\":{\"type\":\"field\",\"field\":\"y\"},\"line_color\":\"#1f77b4\",\"line_alpha\":0.2,\"fill_color\":\"#1f77b3\",\"fill_alpha\":0.2,\"hatch_alpha\":0.2}}}},{\"type\":\"object\",\"name\":\"GlyphRenderer\",\"id\":\"p1211\",\"attributes\":{\"data_source\":{\"type\":\"object\",\"name\":\"ColumnDataSource\",\"id\":\"p1202\",\"attributes\":{\"selected\":{\"type\":\"object\",\"name\":\"Selection\",\"id\":\"p1204\",\"attributes\":{\"indices\":[],\"line_indices\":[]}},\"selection_policy\":{\"type\":\"object\",\"name\":\"UnionRenderers\",\"id\":\"p1203\"},\"data\":{\"type\":\"map\",\"entries\":[[\"index\",{\"type\":\"ndarray\",\"array\":{\"type\":\"bytes\",\"data\":\"AAAAAAEAAAACAAAAAwAAAAQAAAAFAAAABgAAAAcAAAAIAAAACQAAAAoAAAALAAAADAAAAA0AAAAOAAAADwAAABAAAAARAAAAEgAAABMAAAAUAAAAFQAAABYAAAAXAAAAGAAAABkAAAAaAAAAGwAAABwAAAAdAAAAHgAAAB8AAAAgAAAAIQAAACIAAAAjAAAAJAAAACUAAAAmAAAAJwAAACgAAAApAAAAKgAAACsAAAAsAAAALQAAAC4AAAAvAAAAMAAAADEAAAAyAAAAMwAAADQAAAA1AAAANgAAADcAAAA4AAAAOQAAADoAAAA7AAAAPAAAAD0AAAA+AAAAPwAAAEAAAABBAAAAQgAAAEMAAABEAAAARQAAAEYAAABHAAAASAAAAEkAAABKAAAASwAAAEwAAABNAAAATgAAAE8AAABQAAAAUQAAAFIAAABTAAAAVAAAAFUAAABWAAAAVwAAAFgAAABZAAAAWgAAAFsAAAA=\"},\"shape\":[92],\"dtype\":\"int32\",\"order\":\"little\"}],[\"mean intensity\",{\"type\":\"ndarray\",\"array\":{\"type\":\"bytes\",\"data\":\"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\"},\"shape\":[92],\"dtype\":\"float64\",\"order\":\"little\"}],[\"area\",{\"type\":\"ndarray\",\"array\":{\"type\":\"bytes\",\"data\":\"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\"},\"shape\":[92],\"dtype\":\"float64\",\"order\":\"little\"}],[\"image number\",{\"type\":\"ndarray\",\"array\":{\"type\":\"bytes\",\"data\":\"AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAgAAAAIAAAACAAAAAgAAAAIAAAACAAAAAgAAAAIAAAACAAAAAwAAAAMAAAADAAAAAwAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAUAAAAFAAAABQAAAAUAAAAFAAAABQAAAAUAAAAFAAAABQAAAAUAAAAFAAAABQAAAAUAAAAFAAAABQAAAAUAAAAGAAAABgAAAAYAAAAGAAAABgAAAAYAAAAHAAAABwAAAAcAAAAHAAAABwAAAAcAAAAHAAAABwAAAAcAAAAHAAAACAAAAAgAAAAIAAAACAAAAAgAAAAIAAAACAAAAAgAAAA=\"},\"shape\":[92],\"dtype\":\"int32\",\"order\":\"little\"}],[\"__dummy_cat\",{\"type\":\"ndarray\",\"array\":[\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \"],\"shape\":[92],\"dtype\":\"object\",\"order\":\"little\"}],[\"__ECDF\",{\"type\":\"ndarray\",\"array\":{\"type\":\"bytes\",\"data\":\"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\"},\"shape\":[92],\"dtype\":\"float64\",\"order\":\"little\"}],[\"__label\",{\"type\":\"ndarray\",\"array\":[\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \"],\"shape\":[92],\"dtype\":\"object\",\"order\":\"little\"}]]}}},\"view\":{\"type\":\"object\",\"name\":\"CDSView\",\"id\":\"p1212\",\"attributes\":{\"filter\":{\"type\":\"object\",\"name\":\"AllIndices\",\"id\":\"p1213\"}}},\"glyph\":{\"type\":\"object\",\"name\":\"Circle\",\"id\":\"p1208\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"mean intensity\"},\"y\":{\"type\":\"field\",\"field\":\"__ECDF\"},\"line_color\":{\"type\":\"value\",\"value\":\"#1f77b3\"},\"fill_color\":{\"type\":\"value\",\"value\":\"#1f77b3\"}}},\"nonselection_glyph\":{\"type\":\"object\",\"name\":\"Circle\",\"id\":\"p1209\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"mean intensity\"},\"y\":{\"type\":\"field\",\"field\":\"__ECDF\"},\"line_color\":{\"type\":\"value\",\"value\":\"#1f77b3\"},\"line_alpha\":{\"type\":\"value\",\"value\":0.1},\"fill_color\":{\"type\":\"value\",\"value\":\"#1f77b3\"},\"fill_alpha\":{\"type\":\"value\",\"value\":0.1},\"hatch_alpha\":{\"type\":\"value\",\"value\":0.1}}},\"muted_glyph\":{\"type\":\"object\",\"name\":\"Circle\",\"id\":\"p1210\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"mean intensity\"},\"y\":{\"type\":\"field\",\"field\":\"__ECDF\"},\"line_color\":{\"type\":\"value\",\"value\":\"#1f77b3\"},\"line_alpha\":{\"type\":\"value\",\"value\":0.2},\"fill_color\":{\"type\":\"value\",\"value\":\"#1f77b3\"},\"fill_alpha\":{\"type\":\"value\",\"value\":0.2},\"hatch_alpha\":{\"type\":\"value\",\"value\":0.2}}}}}],\"toolbar\":{\"type\":\"object\",\"name\":\"Toolbar\",\"id\":\"p1150\",\"attributes\":{\"tools\":[{\"type\":\"object\",\"name\":\"PanTool\",\"id\":\"p1178\"},{\"type\":\"object\",\"name\":\"WheelZoomTool\",\"id\":\"p1179\"},{\"type\":\"object\",\"name\":\"BoxZoomTool\",\"id\":\"p1180\",\"attributes\":{\"overlay\":{\"type\":\"object\",\"name\":\"BoxAnnotation\",\"id\":\"p1181\",\"attributes\":{\"syncable\":false,\"level\":\"overlay\",\"visible\":false,\"left_units\":\"canvas\",\"right_units\":\"canvas\",\"bottom_units\":\"canvas\",\"top_units\":\"canvas\",\"line_color\":\"black\",\"line_alpha\":1.0,\"line_width\":2,\"line_dash\":[4,4],\"fill_color\":\"lightgrey\",\"fill_alpha\":0.5}}}},{\"type\":\"object\",\"name\":\"SaveTool\",\"id\":\"p1182\"},{\"type\":\"object\",\"name\":\"ResetTool\",\"id\":\"p1183\"},{\"type\":\"object\",\"name\":\"HelpTool\",\"id\":\"p1184\"}]}},\"toolbar_location\":\"above\",\"left\":[{\"type\":\"object\",\"name\":\"LinearAxis\",\"id\":\"p1171\",\"attributes\":{\"ticker\":{\"type\":\"object\",\"name\":\"BasicTicker\",\"id\":\"p1174\",\"attributes\":{\"mantissas\":[1,2,5]}},\"formatter\":{\"type\":\"object\",\"name\":\"BasicTickFormatter\",\"id\":\"p1172\"},\"axis_label\":\"ECDF\",\"major_label_policy\":{\"type\":\"object\",\"name\":\"AllLabels\",\"id\":\"p1173\"}}}],\"below\":[{\"type\":\"object\",\"name\":\"LinearAxis\",\"id\":\"p1164\",\"attributes\":{\"ticker\":{\"type\":\"object\",\"name\":\"BasicTicker\",\"id\":\"p1167\",\"attributes\":{\"mantissas\":[1,2,5]}},\"formatter\":{\"type\":\"object\",\"name\":\"BasicTickFormatter\",\"id\":\"p1165\"},\"axis_label\":\"mean intensity (a.u.)\",\"major_label_policy\":{\"type\":\"object\",\"name\":\"AllLabels\",\"id\":\"p1166\"}}}],\"center\":[{\"type\":\"object\",\"name\":\"Grid\",\"id\":\"p1170\",\"attributes\":{\"axis\":{\"id\":\"p1164\"}}},{\"type\":\"object\",\"name\":\"Grid\",\"id\":\"p1177\",\"attributes\":{\"dimension\":1,\"axis\":{\"id\":\"p1171\"}}}]}},{\"type\":\"object\",\"name\":\"Figure\",\"id\":\"p1214\",\"attributes\":{\"width\":300,\"height\":200,\"x_range\":{\"type\":\"object\",\"name\":\"DataRange1d\",\"id\":\"p1216\"},\"y_range\":{\"type\":\"object\",\"name\":\"DataRange1d\",\"id\":\"p1215\"},\"x_scale\":{\"type\":\"object\",\"name\":\"LinearScale\",\"id\":\"p1227\"},\"y_scale\":{\"type\":\"object\",\"name\":\"LinearScale\",\"id\":\"p1229\"},\"title\":{\"type\":\"object\",\"name\":\"Title\",\"id\":\"p1218\"},\"renderers\":[{\"type\":\"object\",\"name\":\"GlyphRenderer\",\"id\":\"p1266\",\"attributes\":{\"data_source\":{\"type\":\"object\",\"name\":\"ColumnDataSource\",\"id\":\"p1260\",\"attributes\":{\"selected\":{\"type\":\"object\",\"name\":\"Selection\",\"id\":\"p1262\",\"attributes\":{\"indices\":[],\"line_indices\":[]}},\"selection_policy\":{\"type\":\"object\",\"name\":\"UnionRenderers\",\"id\":\"p1261\"},\"data\":{\"type\":\"map\",\"entries\":[[\"x\",[0.53295136,0.53295136,0.53295136,0.53295136,0.53295136,0.53295136,0.64267664,0.64267664,0.64267664,0.64267664,0.7367268800000001,0.7367268800000001,0.7367268800000001,0.7367268800000001,1.2814345200000001,1.2814345200000001,1.3127846,1.3127846,1.3127846,1.3127846,1.3558909600000002,1.3558909600000002,1.35980972,1.35980972,1.3676472400000002,1.3676472400000002,1.3676472400000002,1.3676472400000002,1.3950785600000002,1.3950785600000002,1.42250988,1.42250988,1.43818492,1.43818492,1.4421036800000002,1.4421036800000002,1.54399144,1.54399144,1.54399144,1.54399144,1.56358524,1.56358524,1.5714227600000001,1.5714227600000001,1.57534152,1.57534152,1.5792602800000002,1.5792602800000002,1.5792602800000002,1.5792602800000002,1.5870978000000002,1.5870978000000002,1.5870978000000002,1.5870978000000002,1.5910165600000001,1.5910165600000001,1.59493532,1.59493532,1.61452912,1.61452912,1.6262854000000002,1.6262854000000002,1.6497979600000001,1.6497979600000001,1.65371672,1.65371672,1.65371672,1.65371672,1.65371672,1.65371672,1.6850668000000002,1.6850668000000002,1.72033564,1.72033564,1.7360106800000001,1.7360106800000001,1.7438482000000002,1.7438482000000002,1.74776696,1.74776696,1.7516857200000002,1.7516857200000002,1.7712795200000002,1.7712795200000002,1.7908733200000002,1.7908733200000002,1.85357348,1.85357348,1.8692485200000002,1.8692485200000002,1.8770860400000002,1.8770860400000002,1.8888423200000002,1.8888423200000002,1.8966798400000002,1.8966798400000002,1.9437049600000003,1.9437049600000003,1.95154248,1.95154248,2.00640512,2.00640512,2.00640512,2.00640512,2.0220801600000002,2.0220801600000002,2.0377552000000003,2.0377552000000003,2.04951148,2.04951148,2.05343024,2.05343024,2.05343024,2.05343024,2.0573490000000003,2.0573490000000003,2.06518652,2.06518652,2.07302404,2.07302404,2.0965366000000003,2.0965366000000003,2.10437412,2.10437412,2.13964296,2.13964296,2.14356172,2.14356172,2.18274932,2.18274932,2.2297744400000004,2.2297744400000004,2.2336932000000003,2.2336932000000003,2.24544948,2.24544948,2.24544948,2.24544948,2.3081496400000003,2.3081496400000003,2.31598716,2.31598716,2.3512560000000002,2.3512560000000002,2.39828112,2.39828112,2.43354996,2.43354996,2.45706252,2.45706252,2.4609812800000004,2.4609812800000004,2.4688188,2.4688188,2.4844938400000003,2.4844938400000003,2.5001688800000004,2.5001688800000004,2.55503152,2.55503152,2.5667878,2.5667878,2.57070656,2.57070656,2.59030036,2.59030036,2.60989416,2.60989416,2.63340672,2.63340672,2.63340672,2.63340672,2.6725943200000004,2.6725943200000004,2.7313757200000004,2.7313757200000004,2.743132,2.743132,2.76664456,2.76664456,2.8724510800000003,2.8724510800000003,2.93907,2.93907,3.6836344000000003,3.6836344000000003,3.6836344000000003,3.6836344000000003,3.6836344000000003,3.6836344000000003,3.24865204,3.24865204,3.24865204,3.24865204,3.0566328,3.0566328,3.0566328,3.0566328,2.93907,2.93907,2.89596364,2.89596364,2.89596364,2.89596364,2.8724510800000003,2.8724510800000003,2.83718224,2.83718224,2.76664456,2.76664456,2.76664456,2.76664456,2.743132,2.743132,2.7313757200000004,2.7313757200000004,2.6921881200000004,2.6921881200000004,2.6921881200000004,2.6921881200000004,2.6725943200000004,2.6725943200000004,2.63340672,2.63340672,2.63340672,2.63340672,2.60989416,2.60989416,2.60989416,2.60989416,2.59030036,2.59030036,2.57070656,2.57070656,2.57070656,2.57070656,2.5667878,2.5667878,2.55503152,2.55503152,2.51192516,2.51192516,2.5001688800000004,2.5001688800000004,2.4844938400000003,2.4844938400000003,2.4688188,2.4688188,2.4609812800000004,2.4609812800000004,2.4609812800000004,2.4609812800000004,2.45706252,2.45706252,2.43354996,2.43354996,2.39828112,2.39828112,2.3512560000000002,2.3512560000000002,2.3316622000000002,2.3316622000000002,2.31598716,2.31598716,2.3081496400000003,2.3081496400000003,2.24544948,2.24544948,2.24544948,2.24544948,2.2336932000000003,2.2336932000000003,2.2297744400000004,2.2297744400000004,2.18274932,2.18274932,2.14356172,2.14356172,2.13964296,2.13964296,2.10437412,2.10437412,2.0965366000000003,2.0965366000000003,2.07302404,2.07302404,2.06518652,2.06518652,2.0573490000000003,2.0573490000000003,2.05343024,2.05343024,2.05343024,2.05343024,2.04951148,2.04951148,2.0377552000000003,2.0377552000000003,2.0220801600000002,2.0220801600000002,2.00640512,2.00640512,2.00640512,2.00640512,1.95154248,1.95154248,1.9437049600000003,1.9437049600000003,1.8966798400000002,1.8966798400000002,1.8888423200000002,1.8888423200000002,1.8770860400000002,1.8770860400000002,1.8692485200000002,1.8692485200000002,1.85357348,1.85357348,1.7908733200000002,1.7908733200000002,1.7712795200000002,1.7712795200000002,1.7516857200000002,1.7516857200000002,1.74776696,1.74776696,1.7360106800000001,1.7360106800000001,1.72033564,1.72033564,1.6850668000000002,1.6850668000000002,1.65371672,1.65371672,1.65371672,1.65371672,1.6497979600000001,1.6497979600000001,1.6262854000000002,1.6262854000000002,1.61452912,1.61452912,1.59493532,1.59493532,1.5870978000000002,1.5870978000000002,1.5870978000000002,1.5870978000000002,1.5792602800000002,1.5792602800000002,1.57534152,1.57534152,1.56358524,1.56358524,1.54399144,1.54399144,1.4421036800000002,1.4421036800000002,1.42250988,1.42250988,1.3950785600000002,1.3950785600000002,1.3676472400000002,1.3676472400000002,1.3558909600000002,1.3558909600000002,1.2814345200000001,1.2814345200000001]],[\"y\",[0.0,0.010869565217391304,0.010869565217391304,0.021739130434782608,0.021739130434782608,0.03260869565217391,0.03260869565217391,0.043478260869565216,0.043478260869565216,0.05434782608695652,0.05434782608695652,0.06521739130434782,0.06521739130434782,0.07608695652173914,0.07608695652173914,0.08695652173913043,0.08695652173913043,0.09782608695652174,0.09782608695652174,0.10869565217391304,0.10869565217391304,0.11956521739130435,0.11956521739130435,0.13043478260869565,0.13043478260869565,0.14130434782608695,0.14130434782608695,0.15217391304347827,0.15217391304347827,0.16304347826086957,0.16304347826086957,0.17391304347826086,0.17391304347826086,0.18478260869565216,0.18478260869565216,0.1956521739130435,0.1956521739130435,0.20652173913043478,0.20652173913043478,0.21739130434782608,0.21739130434782608,0.22826086956521738,0.22826086956521738,0.2391304347826087,0.2391304347826087,0.25,0.25,0.2608695652173913,0.2608695652173913,0.2717391304347826,0.2717391304347826,0.2826086956521739,0.2826086956521739,0.29347826086956524,0.29347826086956524,0.30434782608695654,0.30434782608695654,0.31521739130434784,0.31521739130434784,0.32608695652173914,0.32608695652173914,0.33695652173913043,0.33695652173913043,0.34782608695652173,0.34782608695652173,0.358695652173913,0.358695652173913,0.3695652173913043,0.3695652173913043,0.3804347826086957,0.3804347826086957,0.391304347826087,0.391304347826087,0.40217391304347827,0.40217391304347827,0.41304347826086957,0.41304347826086957,0.42391304347826086,0.42391304347826086,0.43478260869565216,0.43478260869565216,0.44565217391304346,0.44565217391304346,0.45652173913043476,0.45652173913043476,0.4673913043478261,0.4673913043478261,0.4782608695652174,0.4782608695652174,0.4891304347826087,0.4891304347826087,0.5,0.5,0.5108695652173914,0.5108695652173914,0.5217391304347826,0.5217391304347826,0.532608695652174,0.532608695652174,0.5434782608695652,0.5434782608695652,0.5543478260869565,0.5543478260869565,0.5652173913043478,0.5652173913043478,0.5760869565217391,0.5760869565217391,0.5869565217391305,0.5869565217391305,0.5978260869565217,0.5978260869565217,0.6086956521739131,0.6086956521739131,0.6195652173913043,0.6195652173913043,0.6304347826086957,0.6304347826086957,0.6413043478260869,0.6413043478260869,0.6521739130434783,0.6521739130434783,0.6630434782608695,0.6630434782608695,0.6739130434782609,0.6739130434782609,0.6847826086956522,0.6847826086956522,0.6956521739130435,0.6956521739130435,0.7065217391304348,0.7065217391304348,0.717391304347826,0.717391304347826,0.7282608695652174,0.7282608695652174,0.7391304347826086,0.7391304347826086,0.75,0.75,0.7608695652173914,0.7608695652173914,0.7717391304347826,0.7717391304347826,0.782608695652174,0.782608695652174,0.7934782608695652,0.7934782608695652,0.8043478260869565,0.8043478260869565,0.8152173913043478,0.8152173913043478,0.8260869565217391,0.8260869565217391,0.8369565217391305,0.8369565217391305,0.8478260869565217,0.8478260869565217,0.8586956521739131,0.8586956521739131,0.8695652173913043,0.8695652173913043,0.8804347826086957,0.8804347826086957,0.8913043478260869,0.8913043478260869,0.9021739130434783,0.9021739130434783,0.9130434782608695,0.9130434782608695,0.9239130434782609,0.9239130434782609,0.9347826086956522,0.9347826086956522,0.9456521739130435,0.9456521739130435,0.9565217391304348,0.9565217391304348,0.967391304347826,0.967391304347826,0.9782608695652174,0.9782608695652174,0.9891304347826086,0.9891304347826086,1.0,1.0,0.9891304347826086,0.9891304347826086,0.9782608695652174,0.9782608695652174,0.967391304347826,0.967391304347826,0.9565217391304348,0.9565217391304348,0.9456521739130435,0.9456521739130435,0.9347826086956522,0.9347826086956522,0.9239130434782609,0.9239130434782609,0.9130434782608695,0.9130434782608695,0.9021739130434783,0.9021739130434783,0.8913043478260869,0.8913043478260869,0.8804347826086957,0.8804347826086957,0.8695652173913043,0.8695652173913043,0.8586956521739131,0.8586956521739131,0.8478260869565217,0.8478260869565217,0.8369565217391305,0.8369565217391305,0.8260869565217391,0.8260869565217391,0.8152173913043478,0.8152173913043478,0.8043478260869565,0.8043478260869565,0.7934782608695652,0.7934782608695652,0.782608695652174,0.782608695652174,0.7717391304347826,0.7717391304347826,0.7608695652173914,0.7608695652173914,0.75,0.75,0.7391304347826086,0.7391304347826086,0.7282608695652174,0.7282608695652174,0.717391304347826,0.717391304347826,0.7065217391304348,0.7065217391304348,0.6956521739130435,0.6956521739130435,0.6847826086956522,0.6847826086956522,0.6739130434782609,0.6739130434782609,0.6630434782608695,0.6630434782608695,0.6521739130434783,0.6521739130434783,0.6413043478260869,0.6413043478260869,0.6304347826086957,0.6304347826086957,0.6195652173913043,0.6195652173913043,0.6086956521739131,0.6086956521739131,0.5978260869565217,0.5978260869565217,0.5869565217391305,0.5869565217391305,0.5760869565217391,0.5760869565217391,0.5652173913043478,0.5652173913043478,0.5543478260869565,0.5543478260869565,0.5434782608695652,0.5434782608695652,0.532608695652174,0.532608695652174,0.5217391304347826,0.5217391304347826,0.5108695652173914,0.5108695652173914,0.5,0.5,0.4891304347826087,0.4891304347826087,0.4782608695652174,0.4782608695652174,0.4673913043478261,0.4673913043478261,0.45652173913043476,0.45652173913043476,0.44565217391304346,0.44565217391304346,0.43478260869565216,0.43478260869565216,0.42391304347826086,0.42391304347826086,0.41304347826086957,0.41304347826086957,0.40217391304347827,0.40217391304347827,0.391304347826087,0.391304347826087,0.3804347826086957,0.3804347826086957,0.3695652173913043,0.3695652173913043,0.358695652173913,0.358695652173913,0.34782608695652173,0.34782608695652173,0.33695652173913043,0.33695652173913043,0.32608695652173914,0.32608695652173914,0.31521739130434784,0.31521739130434784,0.30434782608695654,0.30434782608695654,0.29347826086956524,0.29347826086956524,0.2826086956521739,0.2826086956521739,0.2717391304347826,0.2717391304347826,0.2608695652173913,0.2608695652173913,0.25,0.25,0.2391304347826087,0.2391304347826087,0.22826086956521738,0.22826086956521738,0.21739130434782608,0.21739130434782608,0.20652173913043478,0.20652173913043478,0.1956521739130435,0.1956521739130435,0.18478260869565216,0.18478260869565216,0.17391304347826086,0.17391304347826086,0.16304347826086957,0.16304347826086957,0.15217391304347827,0.15217391304347827,0.14130434782608695,0.14130434782608695,0.13043478260869565,0.13043478260869565,0.11956521739130435,0.11956521739130435,0.10869565217391304,0.10869565217391304,0.09782608695652174,0.09782608695652174,0.08695652173913043,0.08695652173913043,0.07608695652173914,0.07608695652173914,0.06521739130434782,0.06521739130434782,0.05434782608695652,0.05434782608695652,0.043478260869565216,0.043478260869565216,0.03260869565217391,0.03260869565217391,0.021739130434782608,0.021739130434782608,0.010869565217391304,0.010869565217391304,0.0]]]}}},\"view\":{\"type\":\"object\",\"name\":\"CDSView\",\"id\":\"p1267\",\"attributes\":{\"filter\":{\"type\":\"object\",\"name\":\"AllIndices\",\"id\":\"p1268\"}}},\"glyph\":{\"type\":\"object\",\"name\":\"Patch\",\"id\":\"p1263\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"x\"},\"y\":{\"type\":\"field\",\"field\":\"y\"},\"line_color\":\"#1f77b4\",\"line_alpha\":0,\"fill_color\":\"#1f77b3\",\"fill_alpha\":0.3}},\"nonselection_glyph\":{\"type\":\"object\",\"name\":\"Patch\",\"id\":\"p1264\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"x\"},\"y\":{\"type\":\"field\",\"field\":\"y\"},\"line_color\":\"#1f77b4\",\"line_alpha\":0.1,\"fill_color\":\"#1f77b3\",\"fill_alpha\":0.1,\"hatch_alpha\":0.1}},\"muted_glyph\":{\"type\":\"object\",\"name\":\"Patch\",\"id\":\"p1265\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"x\"},\"y\":{\"type\":\"field\",\"field\":\"y\"},\"line_color\":\"#1f77b4\",\"line_alpha\":0.2,\"fill_color\":\"#1f77b3\",\"fill_alpha\":0.2,\"hatch_alpha\":0.2}}}},{\"type\":\"object\",\"name\":\"GlyphRenderer\",\"id\":\"p1278\",\"attributes\":{\"data_source\":{\"type\":\"object\",\"name\":\"ColumnDataSource\",\"id\":\"p1269\",\"attributes\":{\"selected\":{\"type\":\"object\",\"name\":\"Selection\",\"id\":\"p1271\",\"attributes\":{\"indices\":[],\"line_indices\":[]}},\"selection_policy\":{\"type\":\"object\",\"name\":\"UnionRenderers\",\"id\":\"p1270\"},\"data\":{\"type\":\"map\",\"entries\":[[\"index\",{\"type\":\"ndarray\",\"array\":{\"type\":\"bytes\",\"data\":\"AAAAAAEAAAACAAAAAwAAAAQAAAAFAAAABgAAAAcAAAAIAAAACQAAAAoAAAALAAAADAAAAA0AAAAOAAAADwAAABAAAAARAAAAEgAAABMAAAAUAAAAFQAAABYAAAAXAAAAGAAAABkAAAAaAAAAGwAAABwAAAAdAAAAHgAAAB8AAAAgAAAAIQAAACIAAAAjAAAAJAAAACUAAAAmAAAAJwAAACgAAAApAAAAKgAAACsAAAAsAAAALQAAAC4AAAAvAAAAMAAAADEAAAAyAAAAMwAAADQAAAA1AAAANgAAADcAAAA4AAAAOQAAADoAAAA7AAAAPAAAAD0AAAA+AAAAPwAAAEAAAABBAAAAQgAAAEMAAABEAAAARQAAAEYAAABHAAAASAAAAEkAAABKAAAASwAAAEwAAABNAAAATgAAAE8AAABQAAAAUQAAAFIAAABTAAAAVAAAAFUAAABWAAAAVwAAAFgAAABZAAAAWgAAAFsAAAA=\"},\"shape\":[92],\"dtype\":\"int32\",\"order\":\"little\"}],[\"mean intensity\",{\"type\":\"ndarray\",\"array\":{\"type\":\"bytes\",\"data\":\"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\"},\"shape\":[92],\"dtype\":\"float64\",\"order\":\"little\"}],[\"area\",{\"type\":\"ndarray\",\"array\":{\"type\":\"bytes\",\"data\":\"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\"},\"shape\":[92],\"dtype\":\"float64\",\"order\":\"little\"}],[\"image number\",{\"type\":\"ndarray\",\"array\":{\"type\":\"bytes\",\"data\":\"AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAgAAAAIAAAACAAAAAgAAAAIAAAACAAAAAgAAAAIAAAACAAAAAwAAAAMAAAADAAAAAwAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAQAAAAEAAAABAAAAAUAAAAFAAAABQAAAAUAAAAFAAAABQAAAAUAAAAFAAAABQAAAAUAAAAFAAAABQAAAAUAAAAFAAAABQAAAAUAAAAGAAAABgAAAAYAAAAGAAAABgAAAAYAAAAHAAAABwAAAAcAAAAHAAAABwAAAAcAAAAHAAAABwAAAAcAAAAHAAAACAAAAAgAAAAIAAAACAAAAAgAAAAIAAAACAAAAAgAAAA=\"},\"shape\":[92],\"dtype\":\"int32\",\"order\":\"little\"}],[\"__dummy_cat\",{\"type\":\"ndarray\",\"array\":[\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \"],\"shape\":[92],\"dtype\":\"object\",\"order\":\"little\"}],[\"__ECDF\",{\"type\":\"ndarray\",\"array\":{\"type\":\"bytes\",\"data\":\"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\"},\"shape\":[92],\"dtype\":\"float64\",\"order\":\"little\"}],[\"__label\",{\"type\":\"ndarray\",\"array\":[\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \",\" \"],\"shape\":[92],\"dtype\":\"object\",\"order\":\"little\"}]]}}},\"view\":{\"type\":\"object\",\"name\":\"CDSView\",\"id\":\"p1279\",\"attributes\":{\"filter\":{\"type\":\"object\",\"name\":\"AllIndices\",\"id\":\"p1280\"}}},\"glyph\":{\"type\":\"object\",\"name\":\"Circle\",\"id\":\"p1275\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"area\"},\"y\":{\"type\":\"field\",\"field\":\"__ECDF\"},\"line_color\":{\"type\":\"value\",\"value\":\"#1f77b3\"},\"fill_color\":{\"type\":\"value\",\"value\":\"#1f77b3\"}}},\"nonselection_glyph\":{\"type\":\"object\",\"name\":\"Circle\",\"id\":\"p1276\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"area\"},\"y\":{\"type\":\"field\",\"field\":\"__ECDF\"},\"line_color\":{\"type\":\"value\",\"value\":\"#1f77b3\"},\"line_alpha\":{\"type\":\"value\",\"value\":0.1},\"fill_color\":{\"type\":\"value\",\"value\":\"#1f77b3\"},\"fill_alpha\":{\"type\":\"value\",\"value\":0.1},\"hatch_alpha\":{\"type\":\"value\",\"value\":0.1}}},\"muted_glyph\":{\"type\":\"object\",\"name\":\"Circle\",\"id\":\"p1277\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"area\"},\"y\":{\"type\":\"field\",\"field\":\"__ECDF\"},\"line_color\":{\"type\":\"value\",\"value\":\"#1f77b3\"},\"line_alpha\":{\"type\":\"value\",\"value\":0.2},\"fill_color\":{\"type\":\"value\",\"value\":\"#1f77b3\"},\"fill_alpha\":{\"type\":\"value\",\"value\":0.2},\"hatch_alpha\":{\"type\":\"value\",\"value\":0.2}}}}}],\"toolbar\":{\"type\":\"object\",\"name\":\"Toolbar\",\"id\":\"p1217\",\"attributes\":{\"tools\":[{\"type\":\"object\",\"name\":\"PanTool\",\"id\":\"p1245\"},{\"type\":\"object\",\"name\":\"WheelZoomTool\",\"id\":\"p1246\"},{\"type\":\"object\",\"name\":\"BoxZoomTool\",\"id\":\"p1247\",\"attributes\":{\"overlay\":{\"type\":\"object\",\"name\":\"BoxAnnotation\",\"id\":\"p1248\",\"attributes\":{\"syncable\":false,\"level\":\"overlay\",\"visible\":false,\"left_units\":\"canvas\",\"right_units\":\"canvas\",\"bottom_units\":\"canvas\",\"top_units\":\"canvas\",\"line_color\":\"black\",\"line_alpha\":1.0,\"line_width\":2,\"line_dash\":[4,4],\"fill_color\":\"lightgrey\",\"fill_alpha\":0.5}}}},{\"type\":\"object\",\"name\":\"SaveTool\",\"id\":\"p1249\"},{\"type\":\"object\",\"name\":\"ResetTool\",\"id\":\"p1250\"},{\"type\":\"object\",\"name\":\"HelpTool\",\"id\":\"p1251\"}]}},\"toolbar_location\":\"above\",\"left\":[{\"type\":\"object\",\"name\":\"LinearAxis\",\"id\":\"p1238\",\"attributes\":{\"ticker\":{\"type\":\"object\",\"name\":\"BasicTicker\",\"id\":\"p1241\",\"attributes\":{\"mantissas\":[1,2,5]}},\"formatter\":{\"type\":\"object\",\"name\":\"BasicTickFormatter\",\"id\":\"p1239\"},\"axis_label\":\"ECDF\",\"major_label_policy\":{\"type\":\"object\",\"name\":\"AllLabels\",\"id\":\"p1240\"}}}],\"below\":[{\"type\":\"object\",\"name\":\"LinearAxis\",\"id\":\"p1231\",\"attributes\":{\"ticker\":{\"type\":\"object\",\"name\":\"BasicTicker\",\"id\":\"p1234\",\"attributes\":{\"mantissas\":[1,2,5]}},\"formatter\":{\"type\":\"object\",\"name\":\"BasicTickFormatter\",\"id\":\"p1232\"},\"axis_label\":\"area (\\u00b5m\\u00b2)\",\"major_label_policy\":{\"type\":\"object\",\"name\":\"AllLabels\",\"id\":\"p1233\"}}}],\"center\":[{\"type\":\"object\",\"name\":\"Grid\",\"id\":\"p1237\",\"attributes\":{\"axis\":{\"id\":\"p1231\"}}},{\"type\":\"object\",\"name\":\"Grid\",\"id\":\"p1244\",\"attributes\":{\"dimension\":1,\"axis\":{\"id\":\"p1238\"}}}]}}]}}],\"callbacks\":{\"type\":\"map\"}}};\n", " const render_items = [{\"docid\":\"8a94197d-836c-44cc-9618-8f6d7bf12ffe\",\"roots\":{\"p1281\":\"e27d76d7-f022-4a9d-9108-aa590fa9b4b5\"},\"root_ids\":[\"p1281\"]}];\n", " root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n", " }\n", " if (root.Bokeh !== undefined) {\n", " embed_document(root);\n", " } else {\n", " let attempts = 0;\n", " const timer = setInterval(function(root) {\n", " if (root.Bokeh !== undefined) {\n", " clearInterval(timer);\n", " embed_document(root);\n", " } else {\n", " attempts++;\n", " if (attempts > 100) {\n", " clearInterval(timer);\n", " console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n", " }\n", " }\n", " }, 10, root)\n", " }\n", "})(window);" ], "application/vnd.bokehjs_exec.v0+json": "" }, "metadata": { "application/vnd.bokehjs_exec.v0+json": { "id": "p1281" } }, "output_type": "display_data" } ], "source": [ "p_mean_int = iqplot.ecdf(\n", " data=df,\n", " cats=None,\n", " q='mean intensity',\n", " conf_int=True,\n", " height=200,\n", " width=300,\n", " x_axis_label='mean intensity (a.u.)'\n", ")\n", "\n", "p_area = iqplot.ecdf(\n", " data=df,\n", " cats=None,\n", " q='area',\n", " conf_int=True,\n", " height=200,\n", " width=300,\n", " x_axis_label='area (µm²)'\n", ")\n", "\n", "bokeh.io.show(\n", " bokeh.layouts.row(p_mean_int, p_area)\n", ")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The mean and standard deviation of the mean intensities (in arbitrary units) are directly computed." ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "mean 0.399901\n", "std 0.101903\n", "Name: mean intensity, dtype: float64" ] }, "execution_count": 8, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df['mean intensity'].agg(['mean', 'std'])" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Let's go ahead and perform 100,000 *in silico* replicates of this experiment to get a confidence interval on our mean and standard deviation of the mean fluorescence intensities." ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "95% of our bootstrapped means lie between 0.38 and 0.42.\n", "95% of our bootstrapped st. devs. lie between 0.06 and 0.14.\n" ] } ], "source": [ "def draw_bs_reps(data, func, size=1):\n", " \"\"\"Draw bootstrap replicates\"\"\"\n", " return np.array(\n", " [func(np.random.choice(data, size=len(data))) for _ in range(size)]\n", " )\n", "\n", "\n", "# Draw bootstrap replicates of mean\n", "bs_reps_mean = draw_bs_reps(mean_ints, func=np.mean, size=100000)\n", "\n", "# Draw bootstrap replicates of standard deviation\n", "bs_reps_std = draw_bs_reps(mean_ints, func=np.std, size=100000)\n", "\n", "# Compute the 97.5% and 2.5% percentiles.\n", "percs_mean = np.percentile(bs_reps_mean, [2.5, 97.5])\n", "percs_std = np.percentile(bs_reps_std, [2.5, 97.5])\n", "\n", "print(\n", " \"95% of our bootstrapped means lie between {0:.2f} and {1:.2f}.\".format(\n", " percs_mean[0], percs_mean[1]\n", " )\n", ")\n", "print(\n", " \"95% of our bootstrapped st. devs. lie between {0:.2f} and {1:.2f}.\".format(\n", " percs_std[0], percs_std[1]\n", " )\n", ")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Computing environment" ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Python implementation: CPython\n", "Python version : 3.11.3\n", "IPython version : 8.12.0\n", "\n", "numpy : 1.24.3\n", "pandas : 1.5.3\n", "skimage : 0.20.0\n", "bokeh : 3.1.1\n", "iqplot : 0.3.3\n", "holoviews : 1.16.2\n", "jupyterlab: 3.6.3\n", "\n" ] } ], "source": [ "%load_ext watermark\n", "%watermark -v -p numpy,pandas,skimage,bokeh,iqplot,holoviews,jupyterlab" ] } ], "metadata": { "anaconda-cloud": {}, "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.11.3" } }, "nbformat": 4, "nbformat_minor": 4 }