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Detecting cells (Cellpose-based Segmenter)

Introduction

This guide explains you how to detect cells using the pipeline with the Cellpose-based Segmenter operation. The operation allows you to run a segmentation operation using a pretrained cellpose model on any dataset. You can use this operation in an analysis pipeline and in combination with all other analysis operations in the software.

Workflow

'ROI selection' arrow to 'Cellpose-based Segmenter' dashed arrow to 'Export data (optional)'

Activating the Sample Pipeline

  1. In the Shortcut Toolbar, click Analysis Panel Application toolbar with menus File Edit View Data Navigation Objects Analysis Extras Window Help and icon buttons.
    Application toolbar row with menu labels 'File Edit View Data Navigation Objects Analysis Extras Window Help' and icon buttons
  2. In the Sample Pipelines list, double-click the Detect cells Using Cellpose-based Segmenter pipeline.
    Document Pipelines panel showing Sample Pipelines list, Detect Cells Using Cellpose-based Segmenter selected
  3. If you have activated a pipeline, it will be replaced by the new one.

You can open the appropriate How-to guide. By hovering over a pipeline, this button Analysis Panel button in Shortcut Toolbar is displayed. When clicking on it, the option Open How to appears.

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