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Electron microscopy / Image analysis / 3D reconstruction

MicroCT

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Screening for overlapping image ranges in subdivided MicroCT data blocks

Posted on 15. June 201919. November 2022by Stefan

For several reasons it can be of interest to identify the identical images in subdivided MicroCT scan data. Easiest is to inspect both consecutive data stacks face to face in Fiji, in order to find the identical images. Drag and Drop the folder with the first image stack onto the Fiji Taskbar. Choose “Use Virtual […]

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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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