https://bbbc.broadinstitute.org/BBBC039 (CC0)
https://bbbc.broadinstitute.org/BBBC041 (CC BY-NC-SA 3.0)
Make sure you have PyTorch installed.
pip install -U celldetection
pip install git+https://github.com/FZJ-INM1-BDA/celldetection.git
Here you can see some examples of how to train a detection model. The examples already include toy data, so you can get started right away.
import celldetection as cd
cd.models.CPNcd.models.CpnU22cd.models.CpnSlimU22cd.models.CpnResUNetcd.models.CpnWideU22cd.models.CpnResNet34FPNcd.models.CpnResNet50FPNcd.models.CpnResNet18FPNcd.models.CpnResNeXt50FPNcd.models.CpnResNet101FPNcd.models.CpnResNet152FPNcd.models.CpnResNeXt101FPNcd.models.CpnResNeXt152FPNcd.models.CpnWideResNet50FPNcd.models.CpnWideResNet101FPNcd.models.CpnMobileNetV3SmallFPNcd.models.CpnMobileNetV3LargeFPN
cd.models.U22cd.models.U17cd.models.U12cd.models.UNetcd.models.WideU22cd.models.SlimU22cd.models.ResUNetcd.models.UNetEncodercd.models.ResNet50UNetcd.models.ResNet18UNetcd.models.ResNet34UNetcd.models.ResNet152UNetcd.models.ResNet101UNetcd.models.ResNeXt50UNetcd.models.ResNeXt152UNetcd.models.ResNeXt101UNetcd.models.WideResNet50UNetcd.models.WideResNet101UNetcd.models.MobileNetV3SmallUNetcd.models.MobileNetV3LargeUNet
cd.models.FPNcd.models.ResNet18FPNcd.models.ResNet34FPNcd.models.ResNet50FPNcd.models.ResNeXt50FPNcd.models.ResNet101FPNcd.models.ResNet152FPNcd.models.ResNeXt101FPNcd.models.ResNeXt152FPNcd.models.WideResNet50FPNcd.models.WideResNet101FPNcd.models.MobileNetV3LargeFPNcd.models.MobileNetV3SmallFPN
cd.models.ResNet18cd.models.ResNet34cd.models.ResNet50cd.models.ResNet101cd.models.ResNet152cd.models.WideResNet50_2cd.models.ResNeXt50_32x4dcd.models.WideResNet101_2cd.models.ResNeXt101_32x8dcd.models.ResNeXt152_32x8d
@article{UPSCHULTE2022102371,
title = {Contour proposal networks for biomedical instance segmentation},
journal = {Medical Image Analysis},
volume = {77},
pages = {102371},
year = {2022},
issn = {1361-8415},
doi = {https://doi.org/10.1016/j.media.2022.102371},
url = {https://www.sciencedirect.com/science/article/pii/S136184152200024X},
author = {Eric Upschulte and Stefan Harmeling and Katrin Amunts and Timo Dickscheid},
keywords = {Cell detection, Cell segmentation, Object detection, CPN},
}
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