Lineage Tracking and Asymmetric Inheritance Patterns of the Diatom Seminavis robusta [DiatomTrack source code]

This repository belongs to the observation experiments for tracking lineages of Seminavis robusta. The connected work reconstructed the lineages and obtained individuals' timing of division and motility. Cells were entrained for 5 days prior under white light with 25 µmol phot / s in a 12:12 hour rhythm. The images were recorded with a modified Leica microscope (DMIL) and 770 nm light source and a band pass filter. Entrainment continued for the time of recording.
The software analyzes images to identify cells within each frame and extract their trajectories. It constructs cell lineages from these trajectories and allows for their subsequent editing. The processed results can be visualized and modified through a user interface. The workflow consists of three main steps: segmentation of raw images, cell tracking, and manual editing. Progress can be saved and reloaded at any stage. Upon completion of the final step, the software outputs at least a video file and a CSV file. The CSV file contains extracted data points organized by frame, along with unique identifiers that assign each point to a cell of a lineage tree.
The corresponding work defined the cell cycle as beginning at the first frame in which a cell was detected and concluding at the frame in which a child was identified.
A full documentation of the software is available under documentation.zip.
Use: Run main.py. For details see User_manual.
License: The tracking implementation adapts the SORT (Simple Online and Realtime Tracking) algorithm of Alex Bewley et al. Accordingly, this repository is distributed under the GPL-3.0 License. See LICENSE for details.