Single-molecule tracking

This package is a compilation of tasks revolving around single molecule tracking in diverse iPSC-derived cell types. It involves image restoration with denoising, cell mask generation, spot detection, tracking and distance feature extractions.

Code was tested on Mac operating systems Intel and Apple Silicon.

Installation

The base dependencies for this project are managed with pixi. Please install pixi into infrastructure/apps/pixi by executing:

export PIXI_HOME="$(pwd)/infrastructure/apps/pixi"
export PIXI_NO_PATH_UPDATE=1
export TMP_DIR="$(pwd)/infrastructure/.tmp_$USER"
mkdir -p "$TMP_DIR"
curl -fsSL https://pixi.sh/install.sh | bash

and initialize your shell accordingly (see below). For detailed installation instructions visit pixi.sh. Installation should run within a few minutes.

Linux

For Linux systems an installation script is provided, which will download and install pixi into the correct location and configure PIXI_CACHE_DIR and TMPDIR environment variables. To run the installation script, execute the following command in your shell from the root of the project:

sh ./install.sh

Initialization

Everytime you open a new shell you need to initialize it with the correct environment variables. You can do this by sourcing the init.sh from the root of the project:

source init.sh

Execution and demo

For Intel Macs, run the code from the main branch, for Apple Silicon Macs run the code from the osxarm64 branch.

Example data and expected output, as well as input parameters for spot detection and tracking, can be found in the 'demo' folder.

To see detailed documentation on the available tasks and how to execute them run:

pixi run show_docs

and open the link.

Each task should run within a few minutes given the provided demo data.