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Basics:

  • Installation
  • GUI
  • Inputs
  • Settings
  • Outputs
  • Models
  • Training
  • OpenVINO

Examples:

  • In a notebook
  • Command line

API Reference:

  • Cellpose API Guide
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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:

Cellpose 2.0

  • paper on biorxiv

  • `talk <https://www.youtube.com/watch?v=3ydtAhfq6H0`_

  • twitter thread

  • human-in-the-loop training protocol video

Cellpose 1.0

  • paper on biorxiv (see figure 1 below) and in nature methods

  • twitter `thread`_

  • Marius’s talk

fig1

Basics:

  • Installation
    • Built-in model directory
    • Common issues
    • Dependencies
  • GUI
    • Starting the GUI
    • Using the GUI
    • Segmentation options
    • Training your own cellpose model
    • Contributing training data
    • Keyboard shortcuts
  • Inputs
    • 3D segmentation
  • Settings
    • Channels
    • Diameter
    • Resample
    • Flow threshold (aka model fit threshold in GUI)
    • Mask threshold
    • 3D settings
  • Outputs
    • _seg.npy output
    • PNG output
    • ROI manager compatible output for ImageJ
    • Plotting functions
  • Models
    • Model Zoo
    • Full built-in models
      • Cytoplasm model (‘cyto’)
      • Nucleus model (‘nuclei’)
      • Cytoplasm 2.0 model (‘cyto2’)
    • Other built-in models
      • TissueNet models
      • LiveCell models
    • User-trained models
  • Training
  • OpenVINO

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

© Copyright 2020, Carsen Stringer & Marius Pachitariu. Revision e6d7d2e7.

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