/TRACMIT

TRACMIT: Algorithm for Single cells on Micropatterns through mITosis

Primary LanguageBatchfileBSD 3-Clause "New" or "Revised" LicenseBSD-3-Clause

TRACMIT: Algorithm for Single cells on Micropatterns through mITosis

Introduction

TRACMIT is written as an ImageJ ActionBar containing ImageJ 1 Macro code. It allows for the tracking and characterization of the mitotic plate's division angle of cells undergoing mitosis on micropatterns.

Repository Contents

  • Readme.md - This file
  • TRACMIT User Guide.pdf - Interface and user guide
  • LICENSE - License file
  • TRACMIT_1.1.ijm - The actual code of TRACMIT, in ActionBar form
  • TRACMIT_Settings_1.1.ijm - A sub-ActionBar that contains methods for setting TRACMIT parameters, as well as a series of wizards to help set most parameters interactively.
  • updateFile.bat - Windows Batch script useful for when updating this repository. Not of use to end users.
  • TRACMIT Default Settings.txt - Text file with all de default settings for TRACMIT, can be loaded using the Load Parameters button.

Installation

Dependencies

After completing the step above make sure that the following update sites are enabled:

  • IBMP-CNRS - Contains the ActionBar Plugin by Jerôme Mutterer
  • PTBIOP - Contains the BIOPLib and attached plugins used for managing TRACMIT's settings and other internals
  • Imagescience - Contains the FeatureJ Laplacian Plugin used by TRACMIT

The simplest way to install TRACMIT is to use the TRACMIT Update site through Fiji:

  1. From Fiji, go to Help > Update...
  2. Select Manage Update Sites
  3. Click on Add Update Site, this will create a new line on the table
  4. Change the Name to "TRACMIT", for clarity's sake
  5. In the URL column, enter or paste http://biop.epfl.ch/TRACMIT/
  6. Click on Close
  7. Finally click on Apply Changes and restart Fiji

After these steps, you should find "TRACMIT_xx" under Plugins > ActionBar > TRACMIT

Use

To test it, you can download a sample dataset from ZENODO with the following DOI. Please see the User Guide if you have questions

DOI

  1. Launch TRACMIT after installation
  2. Locate the TRACMIT Default Settings.txt in plugins/ActionBar/TRACMIT/ or download it from this repository
  3. Using the Load Parameters button, load the file above.
  4. Click on Select Image and point it to the folder you just extracted.
  5. Select one of the images
  6. For testing, we recommend you crop the image to a more manageable size (512x512).
  7. Click on Measure Current Image

License

This software is offered under the "Revised BSD License" which is described in the LICENCE file contained within this repository.