This dataset contains research data as presented in: Vogelbacher, M.; Strehmann, F.; Bellafkir, H.; Mühling, M.; Korfhage, N.; Schneider, D.; Rösner, S.; Schabo, D. G.; Farwig, N.; Freisleben, B. Identifying and Counting Avian Blood Cells in Whole Slide Images via Deep Learning. Submitted for publication. 2024. In this article, we present a novel approach to automatically quantify avian red and white blood cells in whole slide images. Our approach is based on two deep neural network models. The first model determines image regions that are suitable for counting blood cells, and the second model is an instance segmentation model that detects the cells in the determined image regions. The region selection model achieves up to 97.3% in terms of the F1 score, and the instance segmentation model achieves up to 90.7% in terms of mean average precision. Our approach helps ornithologists to acquire hematological data from avian blood smears more precisely and efficiently. The data published here include the raw annotated data as well as the trained models for the automated counting of blood cells in avian blood smears. Our code is publicly available at https://github.com/umr-ds/avibloodcount.
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AuthorsVogelbacher, Markus
ContributorsStrehmann, Finja
Bellafkir, Hicham
Mühling, Markus
Korfhage, Nikolaus
Schneider, Daniel
Rösner, Sascha
Schabo, Dana G.
Farwig, Nina
Freisleben, Bernd
RelationshipIs Referenced By: (URL) https://github.com/umr-ds/avibloodcount
LicenseCreative Commons Attribution-NonCommercial 4.0
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NameFormatSizeChecksum (MD5)
README.txt .txt3.165Kbc3db41d8f8df19ca455bc4d30c9759a7
dataset_countability.tar .tar2.950Gbf0b971cc294109b7020a4953867f54c2
dataset_segmentation.tar .tar1.929Gbe7d5c79c7aa136b5de835b3538ef761e
efficientNet_B0.onnx .onnx15.99Mb0023d645390f1574ba21b8b72e2b4708
condInst_R101.pth .pth442.6Mb6027ca87982b14b259860e59e5400baa
license_CC-BY-NC-4.0.txt .txt18.88Kbd882379f6314cc023ed84088401bbde8
Creative Commons Attribution-NonCommercial 4.0
Except where otherwise noted, this item's license is described as Creative Commons Attribution-NonCommercial 4.0