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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' box arrow to 'Cellpose-based Segmenter' box; dashed arrow to 'Export data (optional)' box

Activating the Sample Pipeline

  1. In the Shortcut Toolbar, click Analysis Panel Toolbar showing menus File Edit View Data Navigation Objects Analysis Extras Window Help and tool icons.
    Analysis panel showing Document Pipelines and Sample Pipelines list with Compartmentalize Cells or Particles highlighted
  2. In the Sample Pipelines list, double-click the Detect cells Using Cellpose-based Segmenter pipeline.
    Analysis pane: Document Pipelines, + New Pipeline button, Sample Pipelines with Detect Cells Using Region Growing highlighted
  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 Hamburger menu icon showing three horizontal lines is displayed. When clicking on it, the option Open How to appears.

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