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X-ray microCT lizard brain data and labels. Trained network using Biomedisa with different number of training datasets.

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Version 3 2025-07-21, 09:39
Version 2 2025-02-10, 08:21
Version 1 2024-07-08, 06:10
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posted on 2025-07-21, 09:39 authored by Tunhe ZhouTunhe Zhou, Yulia Dragunova, Zegni Triki
<p dir="ltr"><b>28_pbo24_100kV9WLE2Obj0p4xBin2t1sP801_recon.zip: </b>X-ray tomography data of a lizard head (<i>Podarcis bocagei</i>) using Zeiss Xradia Versa 520 at Stockholm University Brain Imaging Center (SUBIC).</p><p dir="ltr"><b>SegmFromDLalgorithm.zip</b>: X-ray microCT (<i>microcomputed tomography</i>) data of lizard heads, cropped down to brain part, and the corresponding labels of brain regions segmented by deep learning algorithm.</p><p dir="ltr"><b>SegmForDLmanual.zip</b>: X-ray microCT data of lizard heads, cropped down to brain part, and the corresponding labels of brain regions segmented semi-manually used as training dataset for deep learning.</p><p dir="ltr"><b>06_recon.zip</b>: an example of original X-ray microCT data of a lizard head before cropping.</p><p dir="ltr">The trained networks below can be used in Biomedisa <a href="https://biomedisa.info/" target="_blank">https://biomedisa.info</a> :</p><p dir="ltr"><b>NetworkTrainedWith5data.tar.h5: </b>trained network using 5 datasets</p><p dir="ltr"><b>NetworkTrainedWith7data.tar.h5</b><b>: </b>trained network using 7 datasets</p><p dir="ltr"><b>NetworkTrainedWith9data.tar.h5</b><b>: </b>trained network using 9 datasets</p><p dir="ltr"><b>NetworkTrainedWith11data.tar.h5</b><b>: </b>trained network using 11 datasets</p>

Funding

This work was financially supported by the Swiss National Science Foundation (No. P400PB_199286 and PZ00P3_209020 to Zegni Triki] and a research grant from The Association for the Study of Animal Behaviour (ASAB) to Zegni Triki. Brain data acquisition was supported by a grant to the Stockholm University Brain Imaging Centre (SU FV-5.1.2-1035-15).

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Associated Publication

T. Zhou, Y. Dragunova, Z. Triki (2024). Brain virtual histology of a lizard species (Podarcis bocagei) using X-ray micro-tomography and deep-learning segmentation. https://doi.org/10.1101/2024.07.05.602071

Affiliation (institution of first SU-affiliated author)

  • 153 Institutionen för lingvistik | Department of Linguistics

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  • public

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  • PUBLIC

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