Manual organelle segmentations (crop345) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse liver acinus (jrc_mus-liver-zon-1)

<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 peroxisome, mitochondria in jrc_mus-liver-zon-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.</p><p dir="ltr"><b>Annotation ID</b>: crop345</p><p dir="ltr"><b>Primary Annotator</b>: Woohyun Park</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>: 32 x 32 x 32 (x, y, z)</p><p dir="ltr"><b>Annotated data dimensions (µm)</b>: 6.4 x 6.4 x 6.4 (x, y, z)</p><p dir="ltr"><b>Annotated data offset (nm)</b>: 106092 x 99276 x 156524 (x, y, z)</p><p dir="ltr"><b>Classes annotated</b>: peroxisome, mitochondria</p><p dir="ltr"><b>Dataset URL</b>: <a href="https://data.janelia.org/51dtOm" rel="noreferrer" target="_blank">s3://janelia-cosem-datasets/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop345</a></p><p dir="ltr"><b>Source (EM) dataset ID</b>: jrc_mus-liver-zon-1</p><p dir="ltr"><b>Source (EM) voxel size (nm)</b>: 8 x 8 x 8 (x, y, z)</p><p dir="ltr"><b>Source (EM) data dimensions (µm)</b>: 210 x 155.73 x 426.69 (x, y, z)</p><p dir="ltr"><b>Source (EM) DOI</b>: <a href="https://doi.org/10.25378/janelia.24135486" rel="noreferrer noopener" target="_blank">https://doi.org/10.25378/janelia.24135486</a></p><p dir="ltr"><b>Visualization website</b>: <a href="https://openorganelle.janelia.org/datasets/jrc_mus-liver-zon-2" rel="noreferrer noopener" target="_blank">https://openorganelle.janelia.org/datasets/jrc_mus-liver-zon-2</a></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>