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Electron microscopy / Image analysis / 3D reconstruction

Arithmetic tool

  • Amira

Extract image data below labels in Amira

Posted on 20. July 201919. November 2022by Stefan

Sometimes it might be of interest to extract the image data below a label for specific purposes (similar to export the image below an area list in TrakEM2). This can be done by attaching the Arithmetic tool to the image data (InputA) and the label field (InputB) and furthermore using the following expression: (B==1)*A+(B!=1)*120 This […]

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  • Amira

Extracting specific labels from label fields in Amira

Posted on 17. July 201930. June 2022by Stefan

In order to post process and visualize single labels individually, they have to be extracted from the label field. This can be done with the Arithmetic tool and the knowledge of the order of labels (0 = exterior, 1 = interior, 2-X = own labels). Attach the Arithmetic tool module to the label field and […]

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About me

Hi, I am Stefan Fischer. I am biologist at the University of Tübingen and Head of Tübingen Structural Microscopy Core Facility (TSM). My methodological interest is set on electron microscopy. Furthermore I do focus on 3D techniques, be it on basis of semi-thin sections (LM), Ultra-thin sections (ssTEM) and also MicroCT data. For that reason I developed a strong interest in open source software packages and image analysis in order to automate (or semi-automate) some of the tedious parts of my workflows.

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new posts

  • Converting MicroCT images from 32bit to 16bit or 8bit in FIJI
  • Amira: Error
  • Exporting ROI-substacks from TrakEM2 with known coordinate positions
  • Extract image data below labels in Amira
  • Extracting specific labels from label fields in Amira

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alignment Amira Arithmetic tool commandline exchange export Fiji Import Label macro memory MicroCT preprocessing ROI selection SEM terminal Trak TrakEM2 ultramicrotomy

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