Data for McGovern et al, 2024: Finding and Following: A deep learning-based pipeline for tracking platelets during thrombus formation in vivo and ex vivo

Data for McGovern et al, 2024: Finding and Following: A deep learning-based pipeline for tracking platelets during thrombus formation in vivo and ex vivoIn these directories you will find example data to run the software described in the paper:segmentationtraining_data: example frames (training_data/training_images) and corresponding ground truth segmentations (training_data/training_gt) that can be used to train the U-net described in the paper.{exvivo,invivo}_example: example images with multiple matching corresponding manual segmentations that can be used to validate the U-net's performance.tracking image datasets that can be segmented with the U-net trained from the segmentation data, then tracked and analysed.The data format is OME-NGFF v0.4, an emerging open format for bioimaging data and metadata. It can therefore be opened with open software in various ecosystems[1]. To open the files in napari, install the napari-ome-zarr plugin and then (for example):napari --plugin napari-ome-zarr tracking/mouse_invivo/200527_IVMTR73_Inj4_saline_exp3.ome.zarrNote, however, that due to a current implementation issue with napari-ome-zarr, the opened segmentation files will not be manually editable with napari. For the moment, use the data loading widget from iterseg if you want to paint into the segmentation data.https://ngff.openmicroscopy.org/tools/ ↩︎

McGovern 等人，2024年：探寻与追随：一种基于深度学习的体内及体外血栓形成过程中血小板追踪的管道。在这些目录中，您可以找到用于运行论文中所述软件的示例数据：
分割训练数据：示例帧（training_data/training_images）以及相应的地面真相分割（training_data/training_gt），可用于训练论文中描述的 U-net。
(exvivo,invivo)_example：具有多个匹配手动分割的示例图像，可用于验证 U-net 的性能。
追踪图像数据集，这些数据集可以使用从分割数据训练出的 U-net 进行分割、追踪和分析。数据格式为 OME-NGFF v0.4，这是一种新兴的开放格式，用于生物成像数据和元数据。因此，它可以被各种生态系统中的开源软件打开[1]。例如，要在 napari 中打开文件，请安装 napari-ome-zarr 插件，然后（例如）：
napari --plugin napari-ome-zarr tracking/mouse_invivo/200527_IVMTR73_Inj4_saline_exp3.ome.zarr
请注意，然而，由于 napari-ome-zarr 当前实施问题，打开的分割文件将无法使用 napari 进行手动编辑。目前，如果您想对分割数据进行绘制，请使用 iterseg 的数据加载小部件。
https://ngff.openmicroscopy.org/tools/