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ZEISS Microscopy Knowledge Base

Detecting big structures automatically

Introduction

This guide explains you how to detect big structures auto using the pipeline with the Intensity Threshold Segmenter operation. The purpose of the pipeline is to detect objects having a random shape and not well-defined borders. It can be applied to any cellular compartments or biological structures.

Workflow

Flowchart of four steps: ROI selection → Denoising → Automatic Threshold → 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 Big Structures Auto Pipeline.
    Analysis panel showing Document Pipelines and Sample Pipelines list with Detect Big Structures Auto 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.

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.
    Software window titled Objects showing an object table with four Segment entries and volumes 256,711; 167,258; 228,431; 243,510
  3. To show the results of each tag, click Single.
  4. For more information, refer to the Online Help (F1).

 

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