Ultrack Advanced Techniques in Neuroimaging 2025 Tutorial

This is ATiNI tutorial on Ultrack, a Python package for large-scale cell tracking under segmentation uncertainty.

Ultrack's visual summary.

The tutorial will be held on Friday, May 2nd, 2025, from 10:30 to 12:00 at the Stanford University.

See left sidebar for the tutorial content.

Goals

There are two goals with this tutorial:

1. Introduce the participants to ultrack package and its capabilities.

2. Show that there are other ways of segmentating and tracking cells rather than training by annotating thousands of cells and applying deep learning models. Pre-trained models and classical algorithms are our friends and can be used to solve many problems.

Notes

Warning

The notebooks are provided as Markdown files (.md) to open them as Jupyter Notebooks, you must right click on the file on your Jupyter interface and select Open with -> Notebook.

Instructors

The instructors for this workshop are:

• Jordão Bragantini

• Teun A.P.M. Huijben

Pre-tutorial setup

Because this is a short tutorial (30 minutes), please download this repository and setup the programming environment before the tutorial starts.

References

• ultrack’s paper

• ultrack’s repository