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v4.0

by z mbstaff

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

  1. Reserve and open a ZMB special B VM.
    • Reserve and open a ZMB special B VM.

    • Search for and open "Anaconda Powershell Prompt (MinicondaZMB)" via the start button.

  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.

  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.

    • 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

Finish Line

Joana Raquel Delgado Martins

Member since: 4/9/19

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48 Guides authored

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ZMB Staff Member of ZMB Staff

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152 Guides authored

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