DOI: 10.5522/04/25715604.v1
title: 3D Microvascular Image Data and Labels for Machine Learning

description: These images and associated binary labels were collected from collaborators across multiple universities to serve as a diverse representation of biomedical images of vessel structures, for use in the training and validation of machine learning tools for vessel segmentation. The dataset contains images from a variety of imaging modalities, at different resolutions, using difference sources of contrast and featuring different organs/ pathologies. This data was use to train, test and validated a foundational model for 3D vessel segmentation, tUbeNet, which can be found on github. The paper descripting the training and validation of the model can be found here. Filenames are structured as follows:  <br>Data - [Modality]_[species Organ]_[resolution].tif Labels - [Modality]_[species Organ]_[resolution]_labels.tif <br>Sub-volumes of larger dataset - [Modality]_[species Organ]_subvolume[dimensions in pixels].tif <br>Manual labelling of blood vessels was carried out using Amira (2020.2, Thermo-Fisher, UK).   <br><b>Training data:</b><b> </b>opticalHREM_murineLiver_2.26x2.26x1.75um.tif: A high resolution episcopic microscopy (HREM) dataset, acquired in house by staining a healthy mouse liver with Eosin B and imaged using a standard HREM protocol.  <i>NB: </i><i>25% of this image volume was with</i><i>h</i><i>e</i><i>l</i><i>d from training, for use as test data</i><i>.</i><i> </i>CT_murineTumour_20x20x20um.tif: X-ray microCT images of a microvascular cast, taken from a subcutaneous mouse model of colorectal cancer (acquired in house). <i>NB: </i><i>25% of this image volume was </i><i>withhe</i><i>ld</i><i> from training, for use as test data</i><i>.</i><i> </i>RSOM_murineTumour_20x20um.tif: Raster-Scanning Optoacoustic Mesoscopy (RSOM) data from a subcutaneous tumour model (provided by Emma Brown, Bohndiek Group, University of Cambridge). The image data has undergone filtering to reduce the background ​(Brown et al., 2019)​.  OCTA_humanRetina_24x24um.tif: retinal angiography data obtained using Optical Coherence Tomography Angiography (OCT-A) (provided by Dr Ranjan Rajendram, Moorfields Eye Hospital). <b>Test data:</b><b> </b>MRI_porcineLiver_0.9x0.9x5mm.tif: T1-weighted Balanced Turbo Field Echo Magnetic Resonance Imaging (MRI) data from a machine-perfused porcine liver, acquired in-house. <b>Test Data</b><b> </b>MFHREM_murineTumourLectin_2.76x2.76x2.61um.tif: a subcutaneous colorectal tumour mouse model was imaged in house using Multi-fluorescence HREM in house, with Dylight 647 conjugated lectin staining the vasculature ​(Walsh et al., 2021)​. The image data has been processed using an asymmetric deconvolution algorithm described by ​Walsh et al., 2020​. NB:<i> </i><i>A sub-volume of 480x480x640 voxels was manually labelled (</i><i>MFHREM_murineTumourLectin_subvolume480x480x640</i><i>.tif</i><i>).</i><i> </i> MFHREM_murineBrainLectin_0.85x0.85x0.86um.tif: an MF-HREM image of the cortex of a mouse brain, stained with Dylight-647 conjugated lectin, was acquired in house ​(Walsh et al., 2021)​. The image data has been downsampled and processed using an asymmetric deconvolution algorithm described by ​Walsh et al., 2020​. <i>NB: </i><i>A sub-volume of </i><i>1000x1000x99</i><i> voxels was manually labelled.</i><i> This sub-volume is provided at full resolution and without preprocessing (</i><i>MFHREM_murineBrainLectin_subvol_0.57x0.57x0.86um</i><i>.tif</i><i>).</i><i> </i> 2Photon_murineOlfactoryBulbLectin_0.2x0.46x5.2um.tif: two-photon data of mouse olfactory bulb blood vessels, labelled with sulforhodamine 101, was kindly provided by Yuxin Zhang at the Sensory Circuits and Neurotechnology Lab, the Francis Crick Institute ​(Bosch et al., 2022)​.  <i>NB: </i><i>A sub-volume of 500x500x79 voxel was manually labelled (</i><i>2Photon_murineOlfactoryBulbLectin_subvolume500x500x79</i><i>.tif</i><i>).</i><i> </i><br><b>References</b><b>:</b><b> </b>​​Bosch, C., Ackels, T., Pacureanu, A., Zhang, Y., Peddie, C. J., Berning, M., Rzepka, N., Zdora, M. C., Whiteley, I., Storm, M., Bonnin, A., Rau, C., Margrie, T., Collinson, L., & Schaefer, A. T. (2022). Functional and multiscale 3D structural investigation of brain tissue through correlative in vivo physiology, synchrotron microtomography and volume electron microscopy. Nature Communications 2022 13:1, 13(1), 1–16. https://doi.org/10.1038/s41467-022-30199-6 ​Brown, E., Brunker, J., & Bohndiek, S. E. (2019). Photoacoustic imaging as a tool to probe the tumour microenvironment. DMM Disease Models and Mechanisms, 12(7). https://doi.org/10.1242/DMM.039636 ​Walsh, C., Holroyd, N. A., Finnerty, E., Ryan, S. G., Sweeney, P. W., Shipley, R. J., & Walker-Samuel, S. (2021). Multifluorescence High-Resolution Episcopic Microscopy for 3D Imaging of Adult Murine Organs. Advanced Photonics Research, 2(10), 2100110. https://doi.org/10.1002/ADPR.202100110 ​Walsh, C., Holroyd, N., Shipley, R., & Walker-Samuel, S. (2020). Asymmetric Point Spread Function Estimation and Deconvolution for Serial-Sectioning Block-Face Imaging. Communications in Computer and Information Science, 1248 CCIS, 235–249. https://doi.org/10.1007/978-3-030-52791-4_19 ​