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

Check out here for a video tutorial introdcuing Cell-ACDC. It is a workshop we held at the I2K Conference 2024.

Sphereoid segmentation

Segment and quantify the spheroid in 3D

Yeast segmentation

Segment, track, and annotate cell cycle

Nuclei segmentation in C. elegans

Segment sub-set of nuclei in multi-cellular organisms

Compute measurements

Easily compute several intesity and morphological measurements

Cell-ACDC launcher

Run batch-processing and utilities from the launcher

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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