v1.0.0 - TrenchRipper release for Zenodo

Same code as previous release (v.1.0.0), but archived with Zenodo.

TrenchRipper v1.0.0 - A Pipeline for High-throughput Mother Machine Image Analysis

This release of TrenchRipper introduces a Python image analysis pipeline optimized for mother machine data and use on high-performance computing (HPC) systems. TrenchRipper automates key image analysis tasks, including:

• Cell Trap Detection: Automatically identifies and localizes cell traps in microscopy images.
• Cell Segmentation: Segments cells with high accuracy (currently only works for fluorescent cytoplasmic markers).
• Lineage Tracing: Tracks full cell lineages using an integer linear program.

Key Features:

• Fully compatible with HPC systems, tested on the O2 High Performance Compute Cluster at Harvard Medical School.
• Outputs segmentation masks, lineage files, and summary statistics for downstream analysis.
• Customizable parameters for different experimental setups.