Need help or advice ? Come to the Icy club ! - Every Wenesday morning from 9h30 to 12h30 - Francois Jacob Building - Main hall - Pasteur
Register

PACT: a Pipeline for Automated Cell Tracking

by bigstudent / Students from the Biomedical Imaging Group (Julien Jacquemot & Clément Marti)

PACT is aimed at dealing with large fluorescence microscopy datasets. It performs a first rough segmentation of cells in a 2D+t/3Dt sequence, then uses parametric snakes to refine it and finally tracks each cell across different frames. It can export cell tracks to the Track Manager.

version 5 (last version):

Download to use and modify in Icy. How do I use protocols ? A Problem ? ask the community.
Changelog for this version: new image

Documentation

Description

Pact: a Pipeline for Automated Cell Tracking lets you track cells in 2D+t datasets (3D+t datasets can be treated by remplacing Active Cells by Active Cells 3D)  . Cell segmentation is performed using active contours, and cell tracking using a nearest-neighbours or a Kalman fileter approach. This protocol implements the whole pipeline and sends the results to the Track Manager so that you can easily add already existing processing stages. The plugins used in the protocol are available separately as  TED The Ellipsoid Detector, Active Cells and Active Cells 3D, and Active Cells Tracker. To assess the protocol performance, a ground truth can be generated using GREG the Graphical Random Ellipsoid Generator. See the documentation of these plugins for a detailed explanation of what the parameters of each plugin do. The segmentation assumes cells are separated and have a roundish shape. Cell division times are not exported.

How to use the protocol

Open the 2D+t sequence you want to process. In TED The Ellipsoid Detector, select the target brightness: BRIGHT if your cell are brighter than the background, DARK if it is the opposite. Select the target brightness in Active Cells too. In Active Cells Tracker set the number of dimensions to TWO. You can fine tune additional parameters in each plugin for better results.

Run the protocol.

Once it is finished, the Track Manager will open and contain the identified tracks. It should look like this:

Tracks viewed in the Track Manager

You can display them over the input sequence, colour them depending on time, extract their velocity profile with the Speed profiler Track Processor, save them in a file and much more depending on the track processors you downloaded.

 


Previous versions:


version 4:

Download to use and modify in Icy.
Changelog for this version: new png

version 3:

Download to use and modify in Icy.
Changelog for this version: changed png to have a nicer display on the website

version 2:

Download to use and modify in Icy.
Changelog for this version: changed png to have a nicer display on the website

version 1:

Download to use and modify in Icy.
Changelog for this version: initial version


Icy protocol publication Id : O9S8Z7