Software for Cell Segmentation, Chemotaxis, and Cell Migration

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 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. 

The FastTrack AI system offers:

  • On-line system with no software to download.
  • Free, no-cost evaluation of a sample movie you provide.
  • Input label free bright-field, phase-contrast, or fluorescent images, it does not matter, we handle it all.
  • Pre-trained, complete pipeline.
  • After uploading images, in a few minutes, you get completed reports and open format data track files.
  • If anything does work to your satisfaction, we fix it.

Sample report here:  sample cell migration report

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 here.

You can get a free evaluation of your movies by emailing – we are happy to do a free evaluation. Then it will only cost you $2/movie for analysis. 

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.

To learn more checkout our main website, our on-line help center, or contact



Option 2: Open Source and Free Software Tools for Cell Segmentation and Cell Migration

Here is a list of open source or free cell segmentation and cell tracking tools that may be useful for cell migration and chemotaxis.

Description Link


ibidi was the first innovator in this space and they have excellent chemotaxis chambers and friendly tech support staff.

ImageJ – the goto tool used by thousands


ImageJ image segmentation

ImageJ manual tracking plugin: Forum 

Scientific Community Image Forum is a discussion forum for scientific image software sponsored by the Center for Open Bioimage Analysis (COBA).

CellProfiler Logo

The CellProfiler project team is based in the Cimini Lab at the Broad Institute of MIT and Harvard. The project was started in 2003 by Anne E. Carpenter and Thouis (Ray) Jones in the Sabatini Laboratory (Whitehead Institute for Biomedical Research) and Golland laboratory (MIT’s CSAIL) and is actively improved and maintained.

Nature paper listing existing tools in the year 2017


A paper from 2021 listing open source segmentation programs useful for machine learning.

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.