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Electron microscopy / Image analysis / 3D reconstruction

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Opening Amira Label files in FIJI

Posted on 7. June 201930. June 2022by Stefan

The import from Amira label files in Fiji allows to access these files without possessing an Amira license (e.g. after a lab change) and to use the labels either in TrakEM2 to plot them on your original data stack (see here) or for general image analysis purposes directly in Fiji. Under “File –> Import” you […]

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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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  • 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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