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ZEISS Microscopy Knowledge Base

Detecting cells or particles

Introduction

This guide explains you how to detect cells or particles using the pipeline with the Blob Finder and Feature Filter operations. The purpose of the pipeline is to detect objects having a quite limited, well defined, structure. The pipeline can be applied to cells, nuclei, or any kind of small particles.

Workflow

Vertical flowchart of four rounded boxes connected by arrows: ROI selection -> Blob Finder -> Segment Filter -> Export data

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 or Particles Pipeline.
    Analysis panel showing Document Pipelines and Sample Pipelines list with Detect Cells or Particles 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 Analysis Panel button in Shortcut Toolbar is displayed. When clicking on it, the option Open How to appears.

Viewing the results

  1. If not already visible, open the Objects dialog. In Shortcut Toolbar, click Objects table Objects window showing table of Segment # entries and Volume (µm³) column values like 0,051; Items: 743 .
  2. Measurements are now visible in the objects table.
    Objects window showing table of Segment entries (Blob Finder - Particles) with volume values and left Filter pane
  3. To add or remove table columns, click Feature Columns...
    For more information, refer to the Online Help (F1).
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