Cell tracking and Transcription sites detection

This codebase is the implementation for the paper "Real-time atlas of nascent RNA kinetics elucidates integrated principles of transcription dynamics".

System Requirements

The code has been tested on:

• Red Hat 8.3.1-5 with CUDA 11.7 (Nvidia L40)
• Ubuntu 18.04 with CUDA 12.2 (Nvidia GeForce RTX 4090)

Environment Setup

Cell segmentation and tracking requires seperate conda environment, with cell-seg.yml and cell-track.yml files provided for each setup.

For cell segmentation, run the following commands to create and install the environment:

cd cell_track
conda env create -f cell-seg.yml
conda activate sam-yolo
cd bash/segment-anything
pip install -e .

Troubleshootings: If there's any issue with mmcv package in usage, suggested to reinstall mmcv using mim instead of pip:

pip uninstall mmcv
mim install "mmcv==2.0.1"

For cell tracking, run the following commands to create and install the environment:

cd cell_track
conda env create -f cell-track.yml
conda activate celltrack

Tips: Environment installation may take a few minutes, depending on your network speed and installation source.

Cell Segmentation and Tracking

Please refer to to README for more details.

Transcription sites Analysis

Please refer to to README for more details.