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: <a href="https://www.biorxiv.org/content/10.1101/2023.10.02.560609" rel="noreferrer" target="_blank">Finding and Following: A deep learning-based pipeline for tracking platelets during thrombus formation in vivo and ex vivo</a><p dir="ltr">In these directories you will find example data to run the software described in the paper:</p><ul><li>segmentation</li><li><ul><li>training_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.</li><li>{exvivo,invivo}_example: example images with multiple matching corresponding manual segmentations that can be used to validate the U-net's performance.</li></ul></li><li>tracking image datasets that can be segmented with the U-net trained from the segmentation data, then tracked and analysed.</li></ul><p dir="ltr">The data format is <a href="https://ngff.openmicroscopy.org/0.4/" rel="noopener" target="_blank">OME-NGFF v0.4</a>, an emerging open format for bioimaging data and metadata. It can therefore be opened with open software in various ecosystems<a href="https://hackmd.io/jCGwsjnvTz6mofUN00rg5w?view#fn1" target="_blank">^[1]</a>. To open the files in napari, install the napari-ome-zarr plugin and then (for example):</p><pre><pre>napari --plugin napari-ome-zarr tracking/mouse_invivo/200527_IVMTR73_Inj4_saline_exp3.ome.zarr<br></pre></pre><p dir="ltr">Note, 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 <a href="https://github.com/AbigailMcGovern/iterseg" rel="noopener" target="_blank">iterseg</a> if you want to paint into the segmentation data.</p><p dir="ltr"><br></p><ol><li><a href="https://ngff.openmicroscopy.org/tools/" rel="noopener" target="_blank">https://ngff.openmicroscopy.org/tools/</a> <a href="https://hackmd.io/jCGwsjnvTz6mofUN00rg5w?view#fnref1" target="_blank">↩︎</a></li></ol><p></p>