DOI: 10.25378/janelia.24247246.v1
title: Manual organelle segmentations (crop158) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse kidney (jrc_mus-kidney)

description: <b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><br><br>- <b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<br><br>- <b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<br><br><b>Annotation description</b>: Dense segmentations of mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, Golgi lumen, Golgi membrane, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, nuclear envelope membrane, cytosol, nucleus, Golgi, endosome, vesicle, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, nuclear envelope, cell, endoplasmic reticulum membrane collective, nuclear envelope membrane collective, mitochondrial ribosome in jrc_mus-kidney 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><br><b>Annotation ID</b>: crop158<br><br><b>Primary Annotator</b>: Woohyun Park<br><br><b>Annotation protocol</b>: Using Amira to manually segment organelles in vEM for machine learning V.3 (http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3)<br><br><b>Software</b>: Amira 3D 2021.1, Classic Segmentation Workroom<br><br><b>Annotated voxel size (nm)</b>: 4 x 4 x 4 (x, y, z)<br><br><b>Annotated data dimensions (µm)</b>: 0.8 x 0.8 x 0.8 (x, y, z)<br><br><b>Annotated data offset (nm)</b>: 51342 x 30430 x 95910 (x, y, z)<br><br><b>Classes annotated</b>: mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, Golgi lumen, Golgi membrane, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, nuclear envelope membrane, cytosol, nucleus, Golgi, endosome, vesicle, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, nuclear envelope, cell, endoplasmic reticulum membrane collective, nuclear envelope membrane collective, mitochondrial ribosome<br><br><b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop158<br><br><b>Source (EM) dataset ID</b>: jrc_mus-kidney<br><br><b>Source (EM) voxel size (nm)</b>: 8 x 8 x 8 (x, y, z)<br><br><b>Source (EM) data dimensions (µm)</b>: 98.3 x 63.81 x 177.59 (x, y, z)<br><br><b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.16913035<br><br><b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-kidney<br><br><b>Publication:</b> <i>CellMap Segmentation Challenge,</i> 2024.<br><br><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.<br><br><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.