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Electron microscopy / Image analysis / 3D reconstruction
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How to open a Zip-Folder of Images in Fiji

Posted on 1. June 201919. November 2022by Stefan

…nothing easier than this: just drag and drop it onto the Fiji Sidebar…

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Aligning an image stack in TrackEM2

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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