Cell-ACDC

A GUI-based Python framework for segmentation, tracking, cell cycle annotations and quantification of microscopy data

Source code on GitHub

Written in Python 3 by Francesco Padovani and Benedikt Mairhoermann.

Tip

If you want a video tutorial as introduction to Cell-ACDC the workshop that we had at the I2K Conference 2024 is available here.

Overview of pipeline and GUI

Contents

• Overview
  • Is it only about segmentation?
• Installation
  • Install stable version
  • Install latest version
  • Install from source (developer version)
• From 0 to Cell-ACDC mastery: A complete guide
  • Running Cell-ACDC
  • The Main Menu
  • Creating Data Structure
  • Preparing data for further analysis (Data-prep)
  • Segmentation and tracking
  • Correcting Tracking and Segmentation Mistakes, Cell Cycle Annotation
• Folder structure
• Create Data Structure with ImageJ/Fiji macros
• How to contribute to Cell-ACDC
  • Development process
• GUI tools
  • File control
  • View options
  • Edit tools: Segmentation and tracking
  • Edit tools: Cell cycle analysis
  • Edit tools: Normal division: Lineage tree
• Models for automatic segmentation and tracking
  • Available models
  • Segmentation models
  • Trackers
  • Adding a new Model
• Scripts to correct shifts in bidirectional scanning
• Cell-ACDC output data
• Troubleshooting
  • Import cv2 failed: ImportError: DLL load failed
• Versions
  • Update v1.2.4
• Scientific publications where Cell-ACDC was used
• Resources
  • Resources
  • Usage
• Citation
  • Segmentation models
  • Trackers

Resources

• GitHub

• Publication

• Forum