cellpose

cellpose is an anatomical segmentation algorithm written in Python 3 by Carsen Stringer and Marius Pachitariu. For support, please open an issue.

We make pip installable releases of cellpose, here is the pypi. You can install it as pip install cellpose[gui].

You can try it out without installing at cellpose.org. Also check out these resources:

• twitter thread

• Marius’s talk on cellpose

• paper on biorxiv (see figure 1 below)

Basics:

• Installation
  • Built-in model directory
  • Common issues
  • Dependencies
• GUI
  • Starting the GUI
  • Using the GUI
  • Segmentation options
  • Contributing training data
• Inputs
  • 3D segmentation
• Settings
  • Channels
    • Cytoplasm model (‘cyto’)
    • Nucleus model (‘nuclei’)
    • Cytoplasm 2.0 model (‘cyto2’)
  • Diameter
  • Resample
  • Flow threshold (aka model fit threshold in GUI)
  • Cell probability threshold
  • 3D settings
• Outputs
  • _seg.npy output
  • PNG output
  • ROI manager compatible output for ImageJ
  • Plotting functions
• Training

Examples:

• In a notebook
• Command line
  • Input settings
  • Run settings
  • Command line examples
  • Options

API Reference:

• Cellpose API Guide
  • Cellpose class
  • CellposeModel
  • SizeModel
  • Metrics
  • Flows to masks
  • Image transforms
  • Plot functions