Manual organelle segmentations (crop452) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of P7 mouse heart (jrc_mus-heart-1)

<p><br></p><p dir="ltr"><b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b></p><ul><li><b>Challenge DOI:</b> <a href="https://doi.org/10.25378/janelia.c.7456966" target="_blank"><u>https://doi.org/10.25378/janelia.c.7456966</u></a></li><li><b>Challenge Website:</b> <a href="https://cellmapchallenge.janelia.org/" target="_blank"><u>https://cellmapchallenge.janelia.org/</u></a></li></ul><p dir="ltr"><b>Annotation description</b>: Dense segmentations of nucleus in jrc_mus-heart-1 using Amira 3D 2021.1, Classic Segmentation Workroom and the 'Using Amira to manually segment organelles in vEM for machine learning V.3' annotation protocol.<br></p><p><br></p><p dir="ltr"><b>Annotation ID</b>: crop452</p><p dir="ltr"><b>Primary Annotator</b>: Aubrey Weigel</p><p dir="ltr"><b>Annotation protocol</b>: Using Amira to manually segment organelles in vEM for machine learning V.3 (<a href="http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3" target="_blank"><u>http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3</u></a>)</p><p dir="ltr"><b>Software</b>: Amira 3D 2021.1, Classic Segmentation Workroom</p><p dir="ltr"><b>Annotated voxel size (nm)</b>: 64 x 64 x 64 (x, y, z)</p><p dir="ltr"><b>Annotated data dimensions (µm)</b>: 24.96 x 25.6 x 25.6 (x, y, z)</p><p dir="ltr"><b>Annotated data offset (nm)</b>: 91996 x 66908 x 33372 (x, y, z)<br></p><p><br></p><p dir="ltr"><b>Classes annotated</b>: nucleus</p><p dir="ltr"><b>Dataset URL</b>: <a href="https://data.janelia.org/5hJS9Y" rel="noreferrer" target="_blank">s3://janelia-cosem-datasets/jrc_mus-heart-1/jrc_mus-heart-1.zarr/recon-1/labels/groundtruth/crop452</a></p><p dir="ltr"><b>Source (EM) dataset ID</b>: jrc_mus-heart-1</p><p dir="ltr"><b>Source (EM) voxel size (nm)</b>: 8 x 8 x 8 (x, y, z)<br></p><p><br></p><p dir="ltr"><b>Source (EM) data dimensions (µm)</b>: 163.23 x 151.69 x 135.87 (x, y, z)<br></p><p><br></p><p dir="ltr"><b>Source (EM) DOI</b>: <a href=" https://doi.org/10.25378/janelia.24020919" rel="noreferrer" target="_blank">https://doi.org/10.25378/janelia.24020919</a></p><p dir="ltr"><b>Visualization website</b>: <a href="https://openorganelle.janelia.org/datasets/jrc_mus-heart-1" rel="noreferrer noopener" target="_blank">https://openorganelle.janelia.org/datasets/jrc_mus-heart-1</a><br></p><p><br></p><p dir="ltr"><b>Publication:</b> <i>CellMap Segmentation Challenge,</i> 2024.</p><p dir="ltr"><b>The CellMap Project Team during this time consisted of:</b> David Ackerman, Davis Bennett, Marley Bryant, Hannah Nguyen, Grace Park, Alyson Petruncio, Alannah Post, Jacquelyn Price, Diana Ramirez, Jeff Rhoades, Rebecca Vorimo, Aubrey Weigel, Marwan Zouinkhi, Yurii Zubov.</p><p dir="ltr"><b>The CellMap Project Team Steering Committee during this time consisted of:</b> Misha Ahrens, Christopher Beck, Teng-Leong Chew, Daniel Feliciano, Jan Funke, Harald Hess, Wyatt Korff, Jennifer Lippincott-Schwartz, Zhe J. Liu, Kayvon Pedram, Stephan Preibisch, Stephan Saalfeld, Ronald Vale, and Aubrey Weigel.</p>