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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

Vertical flowchart: ROI selection → Denoising → Automatic Threshold → Segment Filter → Export data

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 Big Structures Auto Pipeline.
    Document Pipelines pane with + New Pipeline button and Sample Pipelines list highlighting Detect Big Structures Auto
  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.

Viewing the results

  1. If not already visible, open the Objects dialog. In Shortcut Toolbar, click Objects table Objects window with Filter and Tags panel and a long list of Segment # entries with Volume, Volume (µm³) values 0,051–0,054 .
  2. Measurements are now visible in the objects table.
    Objects window showing tag 'Big structures filtered by Volume' and table of three Segment # volumes: 635,654; 657,581; 1007,726
  3. To show the results of each tag, click Single.
  4. For more information, refer to the Online Help (F1).

 

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