Cellpose

Written By: Joana Raquel Delgado Martins (and one other contributor)

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Difficulty

Moderate

Steps

Time Required

Suggest a time??

Introduction

3D segmentation

Tiffs with multiple planes and multiple channels are supported in the GUI (can drag-and-drop tiffs) and supported when running in a notebook. Multiplane images should be of shape nplanes x channels x nY x nX or as nplanes x nY x nX. You can test this by running in python

Step 1 Cellpose

Reserve and open a ZMB special B VM.
Search for and open "Anaconda Powershell Prompt (MinicondaZMB)" via the start button.

Step 2

Check if the "zmb_cellpose" or "zmb_cellpose_v4" environment is available:

Check if the "zmb_cellpose" or "zmb_cellpose_v4" environment is available:
conda info --envs
Note: There are different environments with different cellpose versions: zmb_cellpose has version 3 installed, and zmb_cellpose_v4 has version 4.
Contact the ZMB staff, if no cellpose environments are listed.
Activate the desired enviroment:
conda activate zmb_cellpose
Sometimes, an error-message appears (see image). This particular message can be ignored.
The environment was activated successfully, if it is listed at the start of the line.

Step 3

Launch the Cellpose GUI with the command:

Launch the Cellpose GUI with the command:
cellpose
Note: To segment 3D images, one needs to launch cellpose in the correct mode:
cellpose --Zstack
You are good to go! Start using cellpose.
More info and detailed instructions can be found here.

Step 4

For best accuracy and runtime performance, resize images so cells are less than 100 pixels across
For multi-channel, multi-Z tiff’s, the expected format is Z x channels x Ly x Lx
CHAN TO SEG: this is the channel in which the cytoplasm or nuclei exist
CHAN2 (OPT): if cytoplasm model is chosen, then choose the nuclear channel for this option