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Detecting big structures manually

Introduction

This guide explains you how to detect big structures manual 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: boxes labeled ROI selection → Denoising → Manual 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 Manual Pipeline.
    Document Pipelines panel showing + New Pipeline button and Sample Pipelines list with Detect Big Structures Manual 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 with left Filter panel and table of four Segment # entries showing Volumes 244,477; 332,721; 350,367; 347,782
  3. To show the results of each tag, click Single.
  4. For more information, refer to the Online Help (F1).

 

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