# Functional causality in regulating cell morphogenesis

> **NIH NIH R35** · UT SOUTHWESTERN MEDICAL CENTER · 2020 · $188,346

## Abstract

Abstract
For almost twenty years the Danuser lab has developed a wide range of software for live microscopy image
analysis, including particle tracking. In a landmark paper in 2008 the lab introduced a versatile algorithmic
platform for the robust tracking of dense fields of interacting and partially unstable particle images. The software,
called u-track, has ever since been defining the state-of-art for particle tracking, which is an ubiquitous task in
the analysis of live microscopy data, from super-resolution and single molecule studies to studies of tissue
development and homeostasis. The algorithmic core of u-track has been adopted by the widely-used
TrackMate/ImageJ and CellProfiler open science software packages, as well as by commercial software
platforms like Imaris and Amira. Nonetheless, u-track retained its popularity as standalone, specialized software
package for particle tracking applications because of numerous advanced features these adoptions did not
include. The lab has made a significant effort in maintaining u-track as a user-friendly package and in supporting
the user community through consultations. Over the past four years the lab has expanded u-track's functionality
for the analysis of time-lapse 3D image stacks, which are becoming more and more ubiquitous thanks to the
rapid development of light-sheet microscopy. Especially with u-track3D many labs will lack the necessary
computing infrastructure for the analysis of these massive data sets, and installation of a specialized open source
software on a departmental or institutional high-performance computing infrastructure can be cumbersome.
Moreover, the burden on our lab of maintaining the u-track platform with appropriate backward and forward
version compatibility has become significant. Therefore, we propose a one year project supplementing the
recently funded MIRA grant R35 GM136428-01 to migrate the current u-track and u-track3D software packages
into a containerized pipeline, called u-trackAll, for platform-agnostic cloud-based and/or local computation.
Specifically we will, Aim 1: Develop u-trackAll combining u-track and u-track3D into a generic particle tracking
platform; Aim 2: Develop u-trackAll as a container-mediated, platform-agonistic workflow; Aim 3: Develop
strategies for hybrid (local + cloud) interactive data visualization. The work will be performed by a project team
composed of the current Danuser lab software engineer and a software engineer in UT Southwestern's
Bioinformatics Core Facility, which employs a group of software developers dedicated to the assembly of open
science software workflows.

## Key facts

- **NIH application ID:** 10165091
- **Project number:** 3R35GM136428-01S1
- **Recipient organization:** UT SOUTHWESTERN MEDICAL CENTER
- **Principal Investigator:** Gaudenz Danuser
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $188,346
- **Award type:** 3
- **Project period:** 2020-05-01 → 2025-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10165091

## Citation

> US National Institutes of Health, RePORTER application 10165091, Functional causality in regulating cell morphogenesis (3R35GM136428-01S1). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10165091. Licensed CC0.

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