{"id":95,"date":"2023-01-11T19:28:00","date_gmt":"2023-01-11T19:28:00","guid":{"rendered":"https:\/\/metavilabs.com\/blog\/?p=95"},"modified":"2023-01-19T20:37:34","modified_gmt":"2023-01-19T20:37:34","slug":"software-for-cell-segmentation-chemotaxis-and-cell-migration","status":"publish","type":"post","link":"https:\/\/metavilabs.com\/blog\/2023\/01\/11\/software-for-cell-segmentation-chemotaxis-and-cell-migration\/","title":{"rendered":"Software for Cell Segmentation, Chemotaxis, and Cell Migration"},"content":{"rendered":"<div class=\"boldgrid-section\">\n<div class=\"container\">\n<div class=\"row\" style=\"padding-bottom: 1px;\">\n<div class=\"col-lg-12 col-md-1 col-xs-12 col-sm-12\">\n<p class=\"\">Two options will be discussed:<\/p>\n<ul class=\"\">\n<li>Option 1: MetaVi Labs AI Backed, 100% Automated Cell Tracking<\/li>\n<li>Option 2: For your convenience, we provide a list of Open Source and Free Software Tools for Cell Segmentation and Cell Migration<\/li>\n<\/ul>\n<h3 class=\"\">Option 1: MetaVi Labs AI Backed, 100% Automated Cell Tracking<\/h3>\n<p class=\"\">Cell segmentation for chemotaxis or cell migration studies is a vexing problem. It can be extremely difficult to eliminate errors due to background noise, variations in focus and many other issues that will arise. MetaVi Labs has received thousands uploads to our system so we have seen it all. We have worked hard over the past number of years to solve these problems for you.&nbsp;<\/p>\n<p class=\"\">The FastTrack AI system offers:<\/p>\n<ul class=\"\">\n<li>On-line system with no software to download.<\/li>\n<li>Free, no-cost evaluation of a sample movie you provide.<\/li>\n<li>Input label free bright-field, phase-contrast, or fluorescent images, it does not matter, we handle it all.<\/li>\n<li>Pre-trained, complete pipeline.<\/li>\n<li>After uploading images, in a few minutes, you get completed reports and open format data track files.<\/li>\n<li>If anything does work to your satisfaction, we fix it.<\/li>\n<\/ul>\n<p class=\"\">Sample report here:&nbsp; <a href=\"https:\/\/metavilabs.com\/sites\/default\/files\/help_center\/images\/chemotaxis\/report.html\">sample cell migration report<\/a><\/p>\n<p class=\"\">We provide a simple drag-and-drop interface and produce results in minutes with very little learning curve. And we have experts on-staff to guide you. Watch the how-to-video <a href=\"https:\/\/metavilabs.com\/sites\/default\/files\/help_center\/index.html\">here<\/a>.<\/p>\n<p class=\"\">You can get a free evaluation of your movies by emailing support@metavilabs.com &#8211; we are happy to do a free evaluation. Then it will only cost you $2\/movie for analysis.&nbsp;<\/p>\n<p class=\"\">So before you invest time and effort into trying out the plethora of open source solutions, save yourself time and head-ache by trying the MetaVi Labs solution for free.<\/p>\n<p class=\"\">To learn more checkout our main <a href=\"http:\/\/www.metavilabs.com\">website<\/a>, our <a href=\"https:\/\/metavilabs.com\/sites\/default\/files\/help_center\/index.html\">on-line help center,<\/a> or contact support@metavilabs.com.<\/p>\n<p class=\"\">&nbsp;<\/p>\n<div style=\"width: 640px;\" class=\"wp-video\"><video class=\"wp-video-shortcode\" id=\"video-95-1\" width=\"640\" height=\"360\" preload=\"metadata\" controls=\"controls\"><source type=\"video\/webm\" src=\"https:\/\/metavilabs.com\/sites\/default\/files\/help_center\/images\/chemotaxis\/images\/Pos1_tracking.webm?_=1\" \/><a href=\"https:\/\/metavilabs.com\/sites\/default\/files\/help_center\/images\/chemotaxis\/images\/Pos1_tracking.webm\">https:\/\/metavilabs.com\/sites\/default\/files\/help_center\/images\/chemotaxis\/images\/Pos1_tracking.webm<\/a><\/video><\/div>\n<p class=\"\">&nbsp;<\/p>\n<h3 class=\"\">Option 2: Open Source and Free Software Tools for Cell Segmentation and Cell Migration<\/h3>\n<p class=\"\">Here is a list of open source or free cell segmentation and cell tracking tools that may be useful for cell migration and chemotaxis.<\/p>\n<table class=\"bg-table table\" style=\"width: 100%; height: 690px;\" data-num-cols=\"2\" data-num-rows=\"6\">\n<thead>\n<tr style=\"height: 42.7031px;\">\n<th class=\"\" style=\"width: 65%; height: 42.7031px;\" data-label=\"Header 1\">Description<\/th>\n<th class=\"\" style=\"width: 40%; height: 42.7031px;\" data-label=\"Header 2\">Link<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr style=\"height: 188.594px;\" data-row=\"1\">\n<td class=\"\" style=\"width: 65%; height: 188.594px;\" data-label=\"Header 1\">\n<p class=\"\"><img loading=\"lazy\" decoding=\"async\" class=\"\" src=\"https:\/\/ibidi.com\/img\/ibidi-logo-1612790238.jpg\" alt=\"ibidi \" width=\"204\" height=\"59\"><\/p>\n<p class=\"\">ibidi was the first innovator in this space and they have excellent chemotaxis chambers and friendly tech support staff.&nbsp;<\/p>\n<\/td>\n<td class=\"\" style=\"width: 40%; height: 188.594px;\" data-label=\"Header 2\">\n<p class=\"\">&nbsp;<\/p>\n<p><a class=\"\" href=\"https:\/\/ibidi.com\/chemotaxis-analysis\/171-chemotaxis-and-migration-tool.html\">https:\/\/ibidi.com\/chemotaxis-analysis\/171-chemotaxis-and-migration-tool.html<\/a><\/td>\n<\/tr>\n<tr style=\"height: 209.812px;\" data-row=\"2\">\n<td class=\"\" style=\"width: 65%; height: 209.812px;\" data-label=\"Header 1\">\n<p class=\"\"><img loading=\"lazy\" decoding=\"async\" class=\"\" src=\"https:\/\/imagej.net\/media\/icons\/imagej2.png\" width=\"91\" height=\"91\"><\/p>\n<p class=\"\">ImageJ &#8211; the goto tool used by thousands<\/p>\n<\/td>\n<td class=\"\" style=\"width: 40%; height: 209.812px;\" data-label=\"Header 2\">&nbsp;<\/p>\n<p class=\"\"><a class=\"\" href=\"https:\/\/imagej.net\/imaging\/segmentation\">ImageJ image segmentation<\/a><\/p>\n<p class=\"\">ImageJ manual tracking plugin:<\/p>\n<p class=\"\"><a href=\"https:\/\/imagej.nih.gov\/ij\/plugins\/track\/track.html\">https:\/\/imagej.nih.gov\/ij\/plugins\/track\/track.html<\/a><\/p>\n<\/td>\n<\/tr>\n<tr style=\"height: 236.547px;\" data-row=\"3\">\n<td class=\"\" style=\"width: 65%; height: 236.547px;\" data-label=\"Header 1\">\n<p class=\"\">&nbsp;<\/p>\n<p class=\"\"><a class=\"\" href=\"https:\/\/forum.image.sc\/\"><img loading=\"lazy\" decoding=\"async\" class=\"\" src=\"https:\/\/global.discourse-cdn.com\/business4\/uploads\/imagej\/original\/2X\/a\/a8bb0afa608549b70f9141516502fe7fb4693171.png\" alt=\"Image.sc Forum\" width=\"154\" height=\"46\"><\/a>&nbsp;<\/p>\n<p class=\"\">Scientific Community Image Forum is a discussion forum for scientific image software sponsored by the Center for Open Bioimage Analysis (COBA).<\/p>\n<\/td>\n<td class=\"\" style=\"width: 40%; height: 236.547px;\" data-label=\"Header 2\">\n<p class=\"\">&nbsp;<\/p>\n<p class=\"\">&nbsp;<\/p>\n<p><a href=\"https:\/\/forum.image.sc\/\">https:\/\/forum.image.sc\/<\/a><\/td>\n<\/tr>\n<tr style=\"height: 236.453px;\" data-row=\"4\">\n<td class=\"\" style=\"width: 65%; height: 236.453px;\" data-label=\"Header 1\"><img loading=\"lazy\" decoding=\"async\" class=\"\" src=\"https:\/\/cellprofiler.org\/files\/files\/cellprofiler\/files\/2017_11_21-cp_logo_black_tm_4.png\" alt=\"CellProfiler Logo\" width=\"225\" height=\"56\"><\/p>\n<p class=\"\">The CellProfiler&nbsp;<a href=\"https:\/\/cimini-lab.broadinstitute.org\/people\" target=\"_blank\" rel=\"noreferrer noopener\">project team<\/a>&nbsp;is based in the&nbsp;<a href=\"https:\/\/cimini-lab.broadinstitute.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">Cimini Lab<\/a>&nbsp;at the Broad Institute of MIT and Harvard. The project was started in 2003 by&nbsp;<a href=\"http:\/\/carpenter-singh-lab.broadinstitute.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">Anne E. Carpenter<\/a>&nbsp;and Thouis (Ray) Jones in the Sabatini Laboratory (Whitehead Institute for Biomedical Research) and Golland laboratory (MIT\u2019s CSAIL) and is actively improved and maintained.<\/p>\n<\/td>\n<td class=\"\" style=\"width: 40%; height: 236.453px;\" data-label=\"Header 2\">\n<p class=\"\">&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<p><a href=\"https:\/\/cellprofiler.org\/\">https:\/\/cellprofiler.org\/<\/a><\/td>\n<\/tr>\n<tr style=\"height: 209.812px;\">\n<td class=\"\" style=\"width: 65%; height: 209.812px;\">\n<p class=\"\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone wp-image-101\" src=\"https:\/\/metavilabs.com\/blog\/wp-content\/uploads\/2023\/01\/paper-300x76.png\" alt=\"\" width=\"414\" height=\"105\" srcset=\"https:\/\/metavilabs.com\/blog\/wp-content\/uploads\/2023\/01\/paper-300x76.png 300w, https:\/\/metavilabs.com\/blog\/wp-content\/uploads\/2023\/01\/paper-1024x261.png 1024w, https:\/\/metavilabs.com\/blog\/wp-content\/uploads\/2023\/01\/paper-768x196.png 768w, https:\/\/metavilabs.com\/blog\/wp-content\/uploads\/2023\/01\/paper-250x64.png 250w, https:\/\/metavilabs.com\/blog\/wp-content\/uploads\/2023\/01\/paper-550x140.png 550w, https:\/\/metavilabs.com\/blog\/wp-content\/uploads\/2023\/01\/paper-800x204.png 800w, https:\/\/metavilabs.com\/blog\/wp-content\/uploads\/2023\/01\/paper-707x180.png 707w, https:\/\/metavilabs.com\/blog\/wp-content\/uploads\/2023\/01\/paper-1178x300.png 1178w, https:\/\/metavilabs.com\/blog\/wp-content\/uploads\/2023\/01\/paper.png 1359w\" sizes=\"auto, (max-width: 414px) 100vw, 414px\" \/><\/p>\n<p class=\"\">Nature paper listing existing tools in the year 2017<\/p>\n<\/td>\n<td class=\"\" style=\"width: 40%; height: 209.812px;\">&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<p class=\"\"><a href=\"https:\/\/www.nature.com\/articles\/srep42383\">https:\/\/www.nature.com\/articles\/srep42383<\/a><\/p>\n<p>&nbsp;<\/td>\n<\/tr>\n<tr style=\"height: 230.016px;\">\n<td class=\"\" style=\"width: 65%; height: 230.016px;\">\n<p class=\"\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone wp-image-111\" src=\"https:\/\/metavilabs.com\/blog\/wp-content\/uploads\/2023\/01\/paper_2021-300x58.png\" alt=\"\" width=\"522\" height=\"101\" srcset=\"https:\/\/metavilabs.com\/blog\/wp-content\/uploads\/2023\/01\/paper_2021-300x58.png 300w, https:\/\/metavilabs.com\/blog\/wp-content\/uploads\/2023\/01\/paper_2021-1024x197.png 1024w, https:\/\/metavilabs.com\/blog\/wp-content\/uploads\/2023\/01\/paper_2021-768x147.png 768w, https:\/\/metavilabs.com\/blog\/wp-content\/uploads\/2023\/01\/paper_2021-1536x295.png 1536w, https:\/\/metavilabs.com\/blog\/wp-content\/uploads\/2023\/01\/paper_2021-250x48.png 250w, https:\/\/metavilabs.com\/blog\/wp-content\/uploads\/2023\/01\/paper_2021-550x106.png 550w, https:\/\/metavilabs.com\/blog\/wp-content\/uploads\/2023\/01\/paper_2021-800x154.png 800w, https:\/\/metavilabs.com\/blog\/wp-content\/uploads\/2023\/01\/paper_2021-937x180.png 937w, https:\/\/metavilabs.com\/blog\/wp-content\/uploads\/2023\/01\/paper_2021-1562x300.png 1562w, https:\/\/metavilabs.com\/blog\/wp-content\/uploads\/2023\/01\/paper_2021.png 1677w\" sizes=\"auto, (max-width: 522px) 100vw, 522px\" \/><\/p>\n<p class=\"\">A paper from 2021 listing open source segmentation programs useful for machine learning.<\/p>\n<\/td>\n<td class=\"\" style=\"width: 40%; height: 230.016px;\">&nbsp;<\/p>\n<p class=\"\"><a href=\"https:\/\/www.molbiolcell.org\/doi\/10.1091\/mbc.E20-10-0660\">https:\/\/www.molbiolcell.org\/doi\/10.1091\/mbc.E20-10-0660<\/a><\/p>\n<\/td>\n<\/tr>\n<tr style=\"height: 292.016px;\">\n<td class=\"\" style=\"width: 65%; height: 292.016px;\">\n<p class=\"\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-120\" src=\"https:\/\/metavilabs.com\/blog\/wp-content\/uploads\/2023\/01\/trackmate.png\" alt=\"\" width=\"248\" height=\"112\"><\/p>\n<p class=\"\">TrackMate has a user-friendly interface that allows for performing tracking, data visualization, editing results and track analysis in a convenient way. TrackMate is distributed in Fiji, integrates well with ImageJ and Fiji tools, and does not require a complex installation procedure.&nbsp;<\/p>\n<\/td>\n<td class=\"\" style=\"width: 40%; height: 292.016px;\">&nbsp;<\/p>\n<p class=\"\">&nbsp;<\/p>\n<p class=\"\">&nbsp;<\/p>\n<p class=\"\"><a href=\"https:\/\/imagej.net\/plugins\/trackmate\/\">https:\/\/imagej.net\/plugins\/trackmate\/<\/a><\/p>\n<p>&nbsp;<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p class=\"\">&nbsp;<\/p>\n<p class=\"\">&nbsp;<\/p>\n<p class=\"\">&nbsp;<\/p>\n<\/div>\n<div class=\"col-lg-12 col-md-11 col-sm-12 col-xs-12\"><\/div>\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Two options will be discussed: Option 1: MetaVi Labs AI Backed, 100% Automated Cell Tracking Option 2: For your convenience, we provide a list of Open Source and Free Software Tools for Cell Segmentation and Cell Migration Option 1: MetaVi Labs AI Backed, 100% Automated Cell Tracking Cell segmentation for chemotaxis or cell migration studies [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-95","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/metavilabs.com\/blog\/wp-json\/wp\/v2\/posts\/95","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/metavilabs.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/metavilabs.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/metavilabs.com\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/metavilabs.com\/blog\/wp-json\/wp\/v2\/comments?post=95"}],"version-history":[{"count":10,"href":"https:\/\/metavilabs.com\/blog\/wp-json\/wp\/v2\/posts\/95\/revisions"}],"predecessor-version":[{"id":122,"href":"https:\/\/metavilabs.com\/blog\/wp-json\/wp\/v2\/posts\/95\/revisions\/122"}],"wp:attachment":[{"href":"https:\/\/metavilabs.com\/blog\/wp-json\/wp\/v2\/media?parent=95"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/metavilabs.com\/blog\/wp-json\/wp\/v2\/categories?post=95"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/metavilabs.com\/blog\/wp-json\/wp\/v2\/tags?post=95"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}