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Mitotic Analysis And Recording System

MAARS (Mitotic Analysis And Recording System) is a Micro-Manager plugin designed to automatically record and analyze fission yeast cells in mitosis on-the-fly. Fiji ops for quantitative post-analysis is also possible.

Code structure

  • maars_lib : core of MAARS, required by other sub-projects
  • maars_bfSeg : segmentation with GUI
  • maars_otf : on-the-fly analysis in Micro-Manager 2.0
  • maars_post : quantitative post-analysis with Fiji ops Dependencies:
    • folder jars/Fiji_deps : dependencies of MAARS required in Fiji
    • folder jars/MM_deps : dependencies of MAARS required in Micro-Manager

I just want to segment my cells

Installation (for basic users)

  1. (You can skip this step if you only need the segmentation but not fluo analysis) Copy MAARS dependencies: copy either jars/Fiji_deps or jars/MM_deps into your Fiji jars folder or ImageJ plugins/jars folder correspondingly.
  2. Copy the the MAARS modules:
    1. Copy the jars/maars_lib_2.0.0-SNAPSHOT.jar into your path_to_Fiji/MM_folder/plugins folder (This is the core module required by all the other modules of MAARS)
    2. If you want to launch MAARS
      • on-the-fly with Micro-Manager (Currently unstable due to updates in version 2.0): copy jars/maars_otf_2.0.0-SNAPSHOT.jar to path_to_Micro_Manager_folder/mmplugins.
      • or with Fiji : Copy jars/maars_post_2.0.0-SNAPSHOT.jar and jars/maars_bfSeg_2.0.0-SNAPSHOT.jar into path_to_Fiji_folder/plugins.

For developers (to update)

  • build-mm.sh : use this script to build Micro-Manager under Linux.

  • mavenized-mm.sh : use this script to update local Maven repository inside repo/. MM jars used are MMJ_, MMCoreJ and MMAcqEngine.

  • update-libs.sh : use Maven to build MAARS and copy all dependencies to jars/. It allows "basic users" to copy the required .jar file to a standard Micro-Manager installation.

  • install.sh : Use to install MAARS plugin and its dependencies to Micro-Manager installation.

  • copyFijiDeps.sh : copy dependencies for running MAARS in Fiji to Fiji_deps folder

  • copyMMDeps.sh : copy dependencies for running MAARS in Micro-Manager to MM_deps folder

License

BSD compatible CeCILL-B License.

Authors

Funding

Tong LI was supported by Ministère de l'enseigenment supérieur et de la recherche

Hadien Mary was supported by the Fondation pour la Recherche Medicale.

Jonathan Fouchard and Simon Cabello were supported by the plan Cancer 2009-2013 ‘Systems Biology’.

This work was funded by the ANR-blanc120601 ‘Chromocatch’ and the plan Cancer 2009–2013 ‘Systems Biology’.

Fondation pour la Recherche Médicale (FRM)

plan cancer 2009 - 2013

Agence Nationale de la Recherche (ANR)

Where is our lab

LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France

http://cbi-toulouse.fr/eng/

About

Fiji/Micro-Manager plugin for Mitotic Analysis And Recording System

Resources

Readme
License
Activity
Custom properties

Stars

2 stars

Watchers

4 watching

Forks

3 forks
Report repository

Releases

Packages

Contributors

Languages

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
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Mitotic Analysis And Recording System
MAARS (Mitotic Analysis And Recording System) is a Micro-Manager plugin designed to automatically record and analyze fission yeast cells in mitosis on-the-fly. Fiji ops for quantitative post-analysis is also possible.
Code structure
  • maars_lib : core of MAARS, required by other sub-projects
  • maars_bfSeg : segmentation with GUI
  • maars_otf : on-the-fly analysis in Micro-Manager 2.0
  • maars_post : quantitative post-analysis with Fiji ops
Dependencies:

    • folder jars/Fiji_deps : dependencies of MAARS required in Fiji
    • folder jars/MM_deps : dependencies of MAARS required in Micro-Manager
I just want to segment my cells
Installation (for basic users)
  1. (You can skip this step if you only need the segmentation but not fluo analysis) Copy MAARS dependencies: copy either jars/Fiji_deps or jars/MM_deps into your Fiji jars folder or ImageJ plugins/jars folder correspondingly.
  2. Copy the the MAARS modules:

    1. Copy the jars/maars_lib_2.0.0-SNAPSHOT.jar into your path_to_Fiji/MM_folder/plugins folder (This is the core module required by all the other modules of MAARS)
    2. If you want to launch MAARS

      • on-the-fly with Micro-Manager (Currently unstable due to updates in version 2.0): copy jars/maars_otf_2.0.0-SNAPSHOT.jar to path_to_Micro_Manager_folder/mmplugins.
      • or with Fiji : Copy jars/maars_post_2.0.0-SNAPSHOT.jar and jars/maars_bfSeg_2.0.0-SNAPSHOT.jar into path_to_Fiji_folder/plugins.
For developers (to update)
  • build-mm.sh : use this script to build Micro-Manager under Linux.
  • mavenized-mm.sh : use this script to update local Maven repository inside repo/. MM jars used are MMJ_, MMCoreJ and MMAcqEngine.
  • update-libs.sh : use Maven to build MAARS and copy all dependencies to jars/. It allows "basic users" to copy the required .jar file to a standard Micro-Manager installation.
  • install.sh : Use to install MAARS plugin and its dependencies to Micro-Manager installation.
  • copyFijiDeps.sh : copy dependencies for running MAARS in Fiji to Fiji_deps folder
  • copyMMDeps.sh : copy dependencies for running MAARS in Micro-Manager to MM_deps folder
License
BSD compatible CeCILL-B License.
Authors
Funding
Tong LI was supported by Ministère de l'enseigenment supérieur et de la recherche
Hadien Mary was supported by the Fondation pour la Recherche Medicale.
Jonathan Fouchard and Simon Cabello were supported by the plan Cancer 2009-2013 ‘Systems Biology’.
This work was funded by the ANR-blanc120601 ‘Chromocatch’ and the plan Cancer 2009–2013 ‘Systems
Biology’.
Fondation pour la Recherche Médicale (FRM)
plan cancer 2009 - 2013
Agence Nationale de la Recherche (ANR)
Where is our lab
LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
http://cbi-toulouse.fr/eng/
About
Fiji/Micro-Manager plugin for Mitotic Analysis And Recording System
Resources
Readme
License
Activity
Custom properties
Stars
2 stars
Watchers
4 watching
Forks
3 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
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TravisCI Build Status
Mitotic Analysis And Recording System
MAARS (Mitotic Analysis And Recording System) is a Micro-Manager plugin designed to automatically record and analyze fission yeast cells in mitosis on-the-fly. Fiji ops for quantitative post-analysis is also possible.
Code structure
  • maars_lib : core of MAARS, required by other sub-projects
  • maars_bfSeg : segmentation with GUI
  • maars_otf : on-the-fly analysis in Micro-Manager 2.0
  • maars_post : quantitative post-analysis with Fiji ops
Dependencies:

    • folder jars/Fiji_deps : dependencies of MAARS required in Fiji
    • folder jars/MM_deps : dependencies of MAARS required in Micro-Manager
I just want to segment my cells
Installation (for basic users)
  1. (You can skip this step if you only need the segmentation but not fluo analysis) Copy MAARS dependencies: copy either jars/Fiji_deps or jars/MM_deps into your Fiji jars folder or ImageJ plugins/jars folder correspondingly.
  2. Copy the the MAARS modules:

    1. Copy the jars/maars_lib_2.0.0-SNAPSHOT.jar into your path_to_Fiji/MM_folder/plugins folder (This is the core module required by all the other modules of MAARS)
    2. If you want to launch MAARS

      • on-the-fly with Micro-Manager (Currently unstable due to updates in version 2.0): copy jars/maars_otf_2.0.0-SNAPSHOT.jar to path_to_Micro_Manager_folder/mmplugins.
      • or with Fiji : Copy jars/maars_post_2.0.0-SNAPSHOT.jar and jars/maars_bfSeg_2.0.0-SNAPSHOT.jar into path_to_Fiji_folder/plugins.
For developers (to update)
  • build-mm.sh : use this script to build Micro-Manager under Linux.
  • mavenized-mm.sh : use this script to update local Maven repository inside repo/. MM jars used are MMJ_, MMCoreJ and MMAcqEngine.
  • update-libs.sh : use Maven to build MAARS and copy all dependencies to jars/. It allows "basic users" to copy the required .jar file to a standard Micro-Manager installation.
  • install.sh : Use to install MAARS plugin and its dependencies to Micro-Manager installation.
  • copyFijiDeps.sh : copy dependencies for running MAARS in Fiji to Fiji_deps folder
  • copyMMDeps.sh : copy dependencies for running MAARS in Micro-Manager to MM_deps folder
License
BSD compatible CeCILL-B License.
Authors
Funding
Tong LI was supported by Ministère de l'enseigenment supérieur et de la recherche
Hadien Mary was supported by the Fondation pour la Recherche Medicale.
Jonathan Fouchard and Simon Cabello were supported by the plan Cancer 2009-2013 ‘Systems Biology’.
This work was funded by the ANR-blanc120601 ‘Chromocatch’ and the plan Cancer 2009–2013 ‘Systems
Biology’.
Fondation pour la Recherche Médicale (FRM)
plan cancer 2009 - 2013
Agence Nationale de la Recherche (ANR)
Where is our lab
LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
http://cbi-toulouse.fr/eng/
About
Fiji/Micro-Manager plugin for Mitotic Analysis And Recording System
Resources
Readme
License
Activity
Custom properties
Stars
2 stars
Watchers
4 watching
Forks
3 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
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TravisCI Build Status
Mitotic Analysis And Recording System
MAARS (Mitotic Analysis And Recording System) is a Micro-Manager plugin designed to automatically record and analyze fission yeast cells in mitosis on-the-fly. Fiji ops for quantitative post-analysis is also possible.
Code structure
  • maars_lib : core of MAARS, required by other sub-projects
  • maars_bfSeg : segmentation with GUI
  • maars_otf : on-the-fly analysis in Micro-Manager 2.0
  • maars_post : quantitative post-analysis with Fiji ops
Dependencies:

    • folder jars/Fiji_deps : dependencies of MAARS required in Fiji
    • folder jars/MM_deps : dependencies of MAARS required in Micro-Manager
I just want to segment my cells
Installation (for basic users)
  1. (You can skip this step if you only need the segmentation but not fluo analysis) Copy MAARS dependencies: copy either jars/Fiji_deps or jars/MM_deps into your Fiji jars folder or ImageJ plugins/jars folder correspondingly.
  2. Copy the the MAARS modules:

    1. Copy the jars/maars_lib_2.0.0-SNAPSHOT.jar into your path_to_Fiji/MM_folder/plugins folder (This is the core module required by all the other modules of MAARS)
    2. If you want to launch MAARS

      • on-the-fly with Micro-Manager (Currently unstable due to updates in version 2.0): copy jars/maars_otf_2.0.0-SNAPSHOT.jar to path_to_Micro_Manager_folder/mmplugins.
      • or with Fiji : Copy jars/maars_post_2.0.0-SNAPSHOT.jar and jars/maars_bfSeg_2.0.0-SNAPSHOT.jar into path_to_Fiji_folder/plugins.
For developers (to update)
  • build-mm.sh : use this script to build Micro-Manager under Linux.
  • mavenized-mm.sh : use this script to update local Maven repository inside repo/. MM jars used are MMJ_, MMCoreJ and MMAcqEngine.
  • update-libs.sh : use Maven to build MAARS and copy all dependencies to jars/. It allows "basic users" to copy the required .jar file to a standard Micro-Manager installation.
  • install.sh : Use to install MAARS plugin and its dependencies to Micro-Manager installation.
  • copyFijiDeps.sh : copy dependencies for running MAARS in Fiji to Fiji_deps folder
  • copyMMDeps.sh : copy dependencies for running MAARS in Micro-Manager to MM_deps folder
License
BSD compatible CeCILL-B License.
Authors
Funding
Tong LI was supported by Ministère de l'enseigenment supérieur et de la recherche
Hadien Mary was supported by the Fondation pour la Recherche Medicale.
Jonathan Fouchard and Simon Cabello were supported by the plan Cancer 2009-2013 ‘Systems Biology’.
This work was funded by the ANR-blanc120601 ‘Chromocatch’ and the plan Cancer 2009–2013 ‘Systems
Biology’.
Fondation pour la Recherche Médicale (FRM)
plan cancer 2009 - 2013
Agence Nationale de la Recherche (ANR)
Where is our lab
LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
http://cbi-toulouse.fr/eng/
About
Fiji/Micro-Manager plugin for Mitotic Analysis And Recording System
Resources
Readme
License
Activity
Custom properties
Stars
2 stars
Watchers
4 watching
Forks
3 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
BranchesTags
Repository files navigation
TravisCI Build Status
Mitotic Analysis And Recording System
MAARS (Mitotic Analysis And Recording System) is a Micro-Manager plugin designed to automatically record and analyze fission yeast cells in mitosis on-the-fly. Fiji ops for quantitative post-analysis is also possible.
Code structure
  • maars_lib : core of MAARS, required by other sub-projects
  • maars_bfSeg : segmentation with GUI
  • maars_otf : on-the-fly analysis in Micro-Manager 2.0
  • maars_post : quantitative post-analysis with Fiji ops
Dependencies:

    • folder jars/Fiji_deps : dependencies of MAARS required in Fiji
    • folder jars/MM_deps : dependencies of MAARS required in Micro-Manager
I just want to segment my cells
Installation (for basic users)
  1. (You can skip this step if you only need the segmentation but not fluo analysis) Copy MAARS dependencies: copy either jars/Fiji_deps or jars/MM_deps into your Fiji jars folder or ImageJ plugins/jars folder correspondingly.
  2. Copy the the MAARS modules:

    1. Copy the jars/maars_lib_2.0.0-SNAPSHOT.jar into your path_to_Fiji/MM_folder/plugins folder (This is the core module required by all the other modules of MAARS)
    2. If you want to launch MAARS

      • on-the-fly with Micro-Manager (Currently unstable due to updates in version 2.0): copy jars/maars_otf_2.0.0-SNAPSHOT.jar to path_to_Micro_Manager_folder/mmplugins.
      • or with Fiji : Copy jars/maars_post_2.0.0-SNAPSHOT.jar and jars/maars_bfSeg_2.0.0-SNAPSHOT.jar into path_to_Fiji_folder/plugins.
For developers (to update)
  • build-mm.sh : use this script to build Micro-Manager under Linux.
  • mavenized-mm.sh : use this script to update local Maven repository inside repo/. MM jars used are MMJ_, MMCoreJ and MMAcqEngine.
  • update-libs.sh : use Maven to build MAARS and copy all dependencies to jars/. It allows "basic users" to copy the required .jar file to a standard Micro-Manager installation.
  • install.sh : Use to install MAARS plugin and its dependencies to Micro-Manager installation.
  • copyFijiDeps.sh : copy dependencies for running MAARS in Fiji to Fiji_deps folder
  • copyMMDeps.sh : copy dependencies for running MAARS in Micro-Manager to MM_deps folder
License
BSD compatible CeCILL-B License.
Authors
Funding
Tong LI was supported by Ministère de l'enseigenment supérieur et de la recherche
Hadien Mary was supported by the Fondation pour la Recherche Medicale.
Jonathan Fouchard and Simon Cabello were supported by the plan Cancer 2009-2013 ‘Systems Biology’.
This work was funded by the ANR-blanc120601 ‘Chromocatch’ and the plan Cancer 2009–2013 ‘Systems
Biology’.
Fondation pour la Recherche Médicale (FRM)
plan cancer 2009 - 2013
Agence Nationale de la Recherche (ANR)
Where is our lab
LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
http://cbi-toulouse.fr/eng/
About
Fiji/Micro-Manager plugin for Mitotic Analysis And Recording System
Resources
Readme
License
Activity
Custom properties
Stars
2 stars
Watchers
4 watching
Forks
3 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
TravisCI Build Status
Mitotic Analysis And Recording System
MAARS (Mitotic Analysis And Recording System) is a Micro-Manager plugin designed to automatically record and analyze fission yeast cells in mitosis on-the-fly. Fiji ops for quantitative post-analysis is also possible.
Code structure
  • maars_lib : core of MAARS, required by other sub-projects
  • maars_bfSeg : segmentation with GUI
  • maars_otf : on-the-fly analysis in Micro-Manager 2.0
  • maars_post : quantitative post-analysis with Fiji ops
Dependencies:

    • folder jars/Fiji_deps : dependencies of MAARS required in Fiji
    • folder jars/MM_deps : dependencies of MAARS required in Micro-Manager
I just want to segment my cells
Installation (for basic users)
  1. (You can skip this step if you only need the segmentation but not fluo analysis) Copy MAARS dependencies: copy either jars/Fiji_deps or jars/MM_deps into your Fiji jars folder or ImageJ plugins/jars folder correspondingly.
  2. Copy the the MAARS modules:

    1. Copy the jars/maars_lib_2.0.0-SNAPSHOT.jar into your path_to_Fiji/MM_folder/plugins folder (This is the core module required by all the other modules of MAARS)
    2. If you want to launch MAARS

      • on-the-fly with Micro-Manager (Currently unstable due to updates in version 2.0): copy jars/maars_otf_2.0.0-SNAPSHOT.jar to path_to_Micro_Manager_folder/mmplugins.
      • or with Fiji : Copy jars/maars_post_2.0.0-SNAPSHOT.jar and jars/maars_bfSeg_2.0.0-SNAPSHOT.jar into path_to_Fiji_folder/plugins.
For developers (to update)
  • build-mm.sh : use this script to build Micro-Manager under Linux.
  • mavenized-mm.sh : use this script to update local Maven repository inside repo/. MM jars used are MMJ_, MMCoreJ and MMAcqEngine.
  • update-libs.sh : use Maven to build MAARS and copy all dependencies to jars/. It allows "basic users" to copy the required .jar file to a standard Micro-Manager installation.
  • install.sh : Use to install MAARS plugin and its dependencies to Micro-Manager installation.
  • copyFijiDeps.sh : copy dependencies for running MAARS in Fiji to Fiji_deps folder
  • copyMMDeps.sh : copy dependencies for running MAARS in Micro-Manager to MM_deps folder
License
BSD compatible CeCILL-B License.
Authors
Funding
Tong LI was supported by Ministère de l'enseigenment supérieur et de la recherche
Hadien Mary was supported by the Fondation pour la Recherche Medicale.
Jonathan Fouchard and Simon Cabello were supported by the plan Cancer 2009-2013 ‘Systems Biology’.
This work was funded by the ANR-blanc120601 ‘Chromocatch’ and the plan Cancer 2009–2013 ‘Systems
Biology’.
Fondation pour la Recherche Médicale (FRM)
plan cancer 2009 - 2013
Agence Nationale de la Recherche (ANR)
Where is our lab
LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
http://cbi-toulouse.fr/eng/
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Fiji/Micro-Manager plugin for Mitotic Analysis And Recording System
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Mitotic Analysis And Recording System
MAARS (Mitotic Analysis And Recording System) is a Micro-Manager plugin designed to automatically record and analyze fission yeast cells in mitosis on-the-fly. Fiji ops for quantitative post-analysis is also possible.
Code structure
  • maars_lib : core of MAARS, required by other sub-projects
  • maars_bfSeg : segmentation with GUI
  • maars_otf : on-the-fly analysis in Micro-Manager 2.0
  • maars_post : quantitative post-analysis with Fiji ops
Dependencies:

    • folder jars/Fiji_deps : dependencies of MAARS required in Fiji
    • folder jars/MM_deps : dependencies of MAARS required in Micro-Manager
I just want to segment my cells
Installation (for basic users)
  1. (You can skip this step if you only need the segmentation but not fluo analysis) Copy MAARS dependencies: copy either jars/Fiji_deps or jars/MM_deps into your Fiji jars folder or ImageJ plugins/jars folder correspondingly.
  2. Copy the the MAARS modules:

    1. Copy the jars/maars_lib_2.0.0-SNAPSHOT.jar into your path_to_Fiji/MM_folder/plugins folder (This is the core module required by all the other modules of MAARS)
    2. If you want to launch MAARS

      • on-the-fly with Micro-Manager (Currently unstable due to updates in version 2.0): copy jars/maars_otf_2.0.0-SNAPSHOT.jar to path_to_Micro_Manager_folder/mmplugins.
      • or with Fiji : Copy jars/maars_post_2.0.0-SNAPSHOT.jar and jars/maars_bfSeg_2.0.0-SNAPSHOT.jar into path_to_Fiji_folder/plugins.
For developers (to update)
  • build-mm.sh : use this script to build Micro-Manager under Linux.
  • mavenized-mm.sh : use this script to update local Maven repository inside repo/. MM jars used are MMJ_, MMCoreJ and MMAcqEngine.
  • update-libs.sh : use Maven to build MAARS and copy all dependencies to jars/. It allows "basic users" to copy the required .jar file to a standard Micro-Manager installation.
  • install.sh : Use to install MAARS plugin and its dependencies to Micro-Manager installation.
  • copyFijiDeps.sh : copy dependencies for running MAARS in Fiji to Fiji_deps folder
  • copyMMDeps.sh : copy dependencies for running MAARS in Micro-Manager to MM_deps folder
License
BSD compatible CeCILL-B License.
Authors
Funding
Tong LI was supported by Ministère de l'enseigenment supérieur et de la recherche
Hadien Mary was supported by the Fondation pour la Recherche Medicale.
Jonathan Fouchard and Simon Cabello were supported by the plan Cancer 2009-2013 ‘Systems Biology’.
This work was funded by the ANR-blanc120601 ‘Chromocatch’ and the plan Cancer 2009–2013 ‘Systems
Biology’.
Fondation pour la Recherche Médicale (FRM)
plan cancer 2009 - 2013
Agence Nationale de la Recherche (ANR)
Where is our lab
LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
http://cbi-toulouse.fr/eng/
About
Fiji/Micro-Manager plugin for Mitotic Analysis And Recording System
Resources
Readme
License
Activity
Custom properties
Stars
2 stars
Watchers
4 watching
Forks
3 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
BranchesTags
Repository files navigation
TravisCI Build Status
Mitotic Analysis And Recording System
MAARS (Mitotic Analysis And Recording System) is a Micro-Manager plugin designed to automatically record and analyze fission yeast cells in mitosis on-the-fly. Fiji ops for quantitative post-analysis is also possible.
Code structure
  • maars_lib : core of MAARS, required by other sub-projects
  • maars_bfSeg : segmentation with GUI
  • maars_otf : on-the-fly analysis in Micro-Manager 2.0
  • maars_post : quantitative post-analysis with Fiji ops
Dependencies:

    • folder jars/Fiji_deps : dependencies of MAARS required in Fiji
    • folder jars/MM_deps : dependencies of MAARS required in Micro-Manager
I just want to segment my cells
Installation (for basic users)
  1. (You can skip this step if you only need the segmentation but not fluo analysis) Copy MAARS dependencies: copy either jars/Fiji_deps or jars/MM_deps into your Fiji jars folder or ImageJ plugins/jars folder correspondingly.
  2. Copy the the MAARS modules:

    1. Copy the jars/maars_lib_2.0.0-SNAPSHOT.jar into your path_to_Fiji/MM_folder/plugins folder (This is the core module required by all the other modules of MAARS)
    2. If you want to launch MAARS

      • on-the-fly with Micro-Manager (Currently unstable due to updates in version 2.0): copy jars/maars_otf_2.0.0-SNAPSHOT.jar to path_to_Micro_Manager_folder/mmplugins.
      • or with Fiji : Copy jars/maars_post_2.0.0-SNAPSHOT.jar and jars/maars_bfSeg_2.0.0-SNAPSHOT.jar into path_to_Fiji_folder/plugins.
For developers (to update)
  • build-mm.sh : use this script to build Micro-Manager under Linux.
  • mavenized-mm.sh : use this script to update local Maven repository inside repo/. MM jars used are MMJ_, MMCoreJ and MMAcqEngine.
  • update-libs.sh : use Maven to build MAARS and copy all dependencies to jars/. It allows "basic users" to copy the required .jar file to a standard Micro-Manager installation.
  • install.sh : Use to install MAARS plugin and its dependencies to Micro-Manager installation.
  • copyFijiDeps.sh : copy dependencies for running MAARS in Fiji to Fiji_deps folder
  • copyMMDeps.sh : copy dependencies for running MAARS in Micro-Manager to MM_deps folder
License
BSD compatible CeCILL-B License.
Authors
Funding
Tong LI was supported by Ministère de l'enseigenment supérieur et de la recherche
Hadien Mary was supported by the Fondation pour la Recherche Medicale.
Jonathan Fouchard and Simon Cabello were supported by the plan Cancer 2009-2013 ‘Systems Biology’.
This work was funded by the ANR-blanc120601 ‘Chromocatch’ and the plan Cancer 2009–2013 ‘Systems
Biology’.
Fondation pour la Recherche Médicale (FRM)
plan cancer 2009 - 2013
Agence Nationale de la Recherche (ANR)
Where is our lab
LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
http://cbi-toulouse.fr/eng/
About
Fiji/Micro-Manager plugin for Mitotic Analysis And Recording System
Resources
Readme
License
Activity
Custom properties
Stars
2 stars
Watchers
4 watching
Forks
3 forks
Report repository
Releases
Packages
Contributors
Languages