Manual organelle segmentations (crop162) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse kidney (jrc_mus-kidney)

This acquisition is part of the CellMap 2024 Segmentation Challenge

- Challenge DOI: https://doi.org/10.25378/janelia.c.7456966

- Challenge Website: https://cellmapchallenge.janelia.org/

Annotation description: Dense segmentations of extracellular space, plasma membrane, mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, euchromatin, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, heterochromatin, nuclear pore in, nuclear pore out, nuclear envelope lumen, nuclear envelope membrane, microtubule out, nucleoplasm, microtubule in, cytosol, nucleus, endosome, vesicle, mitochondria, endoplasmic reticulum, nuclear envelope, nuclear pore, chromatin, microtubule, cell, endoplasmic reticulum membrane collective, nuclear envelope membrane collective 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.

Annotation ID: crop162

Primary Annotator: Alyson Petruncio

Annotation protocol: Using Amira to manually segment organelles in vEM for machine learning V.3 (http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3)

Software: Amira 3D 2021.1, Classic Segmentation Workroom

Annotated voxel size (nm): 4 x 4 x 4 (x, y, z)

Annotated data dimensions (µm): 0.8 x 0.8 x 0.8 (x, y, z)

Annotated data offset (nm): 38144 x 56816 x 84400 (x, y, z)

Classes annotated: extracellular space, plasma membrane, mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, euchromatin, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, heterochromatin, nuclear pore in, nuclear pore out, nuclear envelope lumen, nuclear envelope membrane, microtubule out, nucleoplasm, microtubule in, cytosol, nucleus, endosome, vesicle, mitochondria, endoplasmic reticulum, nuclear envelope, nuclear pore, chromatin, microtubule, cell, endoplasmic reticulum membrane collective, nuclear envelope membrane collective

Dataset URL: s3://janelia-cosem-datasets/jrc_mus-kidney/jrc_mus-kidney.zarr/recon-1/labels/groundtruth/crop162

Source (EM) dataset ID: jrc_mus-kidney

Source (EM) voxel size (nm): 8 x 8 x 8 (x, y, z)

Source (EM) data dimensions (µm): 98.3 x 63.81 x 177.59 (x, y, z)

Source (EM) DOI: https://doi.org/10.25378/janelia.16913035

Visualization website: https://openorganelle.janelia.org/datasets/jrc_mus-kidney

Publication: CellMap Segmentation Challenge, 2024.

The CellMap Project Team during this time consisted of: 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.

The CellMap Project Team Steering Committee during this time consisted of: 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.