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Electron microscopy / Image analysis / 3D reconstruction

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Selecting several images in TrakEM2

Posted on 9. June 201918. November 2022by Stefan

For several reasons it can be helpful to be able to select only a range of images within the image stack in TrakEM2. For example to link those images in order to manually rotate them (see here). A selection of images is done via “right-click in canvas” –> Selection –> Select all that match Start 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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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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