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@@ -1,7 +1,22 @@
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# AIDAhisto_Files
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-Atlas and test images required for AIDAhisto
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+Atlas and test images required for [AIDAhisto](https://github.com/aswendtlab/AIDAhisto).
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-\item[\textbf{ARA}] Contains the atlas in 10um and 50um with parental and original regions. Each atlas is also in a split version to distinguish the cell count between the left and right hemisphere. Furthermore, the acronyms are included that correspond to those of the Allen Brain Institute
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+## Files:
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+**ARA:**
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+Contains the atlas in 10 um and 50 um resolution in the original, parental (_parent) and (_splitted) version as well as the list of acronyms. The parental version includes less regions (functional regions were summarized according to the Allen ontology, see details in the related [AIDAmri](https://doi.org/10.3389/fninf.2019.00042) publication). The splitted version contains the atlas with different grey values per hemisphere to distinguish left and right side. Original files were obtained from: [Allen Mouse Brain Atlas](https://www.nature.com/articles/nature05453)[ (CCFv3)](http://help.brain-map.org/display/mousebrain/Documentation).
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+**ARA_SC:**
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+Contains custom vector files, which were manually drawn from the original [Allen Mouse Spinal Cord Atlas](https://mousespinal.brain-map.org) images (C1-8, T1-2 level). Note! Splitted version available only (with grey values to distinguish left and right side.
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+**Test_Images/Test_Images_SC:**
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+Contains sample images of different staining (GFAP, IBA1) with different resolutions of brain or spinal cord (SC) sections. There is also an already transformed atlas in original version *wholebrainatlas.tif* and split version *wholebrain\atlas\splitted.tif* which is overlaid with the brain slice *wholebrainslice.tif*. The results after the processing are described in detail in the [AIDAhisto manual](https://github.com/aswendtlab/AIDAhisto/AIDAhisto_Manual).
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+## Authors:
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+Annika Vohn, Ann-Sophie Benz, Markus Aswendt.
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+Data made available through the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International Public License.
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-\item[\textbf{testImages}] Contains sample images of different staining (GFAP, IBA1) with different resolutions. There is also an already transformed atlas in original version {\tt wholebrain\_atlas.tif} and split version {\tt wholebrain\_atlas\_splitted.tif} which is overlaid with the brain slice {\tt wholebrain\_slice.tif}. The results after the processing are described in detail in the manual.pdf. Those who process these images are listed in the logfile {\tt wholebrain\_slice.tif\_process.log} \end{itemize}
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