cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25378/janelia.24247102.v1
title: Manual organelle segmentations (crop138) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse liver (jrc_mus-liver)

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, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, cytosol, endosome, vesicle, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective in jrc_mus-liver 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>: crop138<br><br><b>Primary Annotator</b>: Alyson Petruncio, Thomson Rymer<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>: 1.6 x 1.6 x 1.6 (x, y, z)<br><br><b>Annotated data offset (nm)</b>: 51998 x 36798 x 63998 (x, y, z)<br><br><b>Classes annotated</b>: mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, cytosol, endosome, vesicle, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective<br><br><b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop138<br><br><b>Source (EM) dataset ID</b>: jrc_mus-liver<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>: 101.98 x 101.82 x 71.46 (x, y, z)<br><br><b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.16913047<br><br><b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-liver<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.
DOI: 10.6084/m9.figshare.c.3625733_d4.v1
title: Additional file 8: Table S7. of Short chain acyl-CoA dehydrogenase deficiency and short-term high-fat diet perturb mitochondrial energy metabolism and transcriptional control of lipid-handling in liver

description: Predicted activation/inhibition of upstream regulators all categories. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.c.3625814_d3.v1
title: Additional file 1: Table S1. of A missense mutation in solute carrier family 12, member 1 (SLC12A1) causes hydrallantois in Japanese Black cattle

description: Primer information for Y chromosome and GAPDH. Table S2.The shared haplotype of hydrallantois in the affected fetuses. Positions are based on the UMD3.1 assembly of the bovine genome. Table S3.Detailed features of CNVs in the critical region of hydrallantois in 1481 Japanese Black cattle. Positions are based on the UMD3.1 assembly of the bovine genome. CNVs were detected from 1481 Japanese Black cattle [17] using the Illumina BovineHD BeadChip Array [15]. 1 loss type of CNV is the deleted type; gain type of CNV is the duplicated type. 2 Haplotypes of 1481 animals were determined by Beagle software. Table S4.Genes within the critical region of hydrallantois in Japanese Black cattle. Positions are based on the UMD3.1 assembly of the bovine genome. Table S5.Primer information for g.62111230G &gt; A and g.62382825G &gt; A. Positions are based on the UMD3.1 assembly of the bovine genome. Table S6.Transcript and protein ID of bovine SLC12A1. Table S7.Genotypes of two variants validated using Sanger sequencing. 1 Phenotype was diagnosed by veterinarians following the standard guidelines and textbooks (for diagnosis criteria, see [1]). 2 Haplotypes were genotyped by GGP_SuperLDv2-0 26 K BeadChip and determined by Beagle software. 3 N = Non-risk-haplotype; Risk = risk-haplotype. Table S8.Primer information for exon of SLC12A1. Positions are based on the UMD3.1 assembly of the bovine genome. Table S9.Bartter syndrome-associated genes and their positions on the UMD3.1 assembly of the bovine genome. Positions are based on the UMD3.1 assembly of the bovine genome. 1 Bartter syndrome type 4B is caused by simultaneous mutations in both the CLCNKA and CLCNKB genes. 2 CLCNKB is not identified or mapped on the UMD3.1 assembly of the bovine genome. 3 Gitelman syndrome is formerly considered a subset of the Bartter syndrome. (XLSX 50 kb)
DOI: 10.6084/m9.figshare.c.3625838_d1.v1
title: Additional file 1: of Efficacy and safety of fluconazole prophylaxis in extremely low birth weight infants: multicenter pre-post cohort study

description: Datasets. Excel data were retrieved from the data repository. (XLS 1976 kb)
DOI: 10.6084/m9.figshare.c.3625838_d2.v1
title: Additional file 2: of Efficacy and safety of fluconazole prophylaxis in extremely low birth weight infants: multicenter pre-post cohort study

description: Data dictionary. The coding IDs, names, sequences and values of each data are described. (XLSX 2247 kb)
DOI: 10.6084/m9.figshare.c.3625862_d1.v1
title: Additional file 4: Matrix S3. of Dengue research networks: building evidence for policy and planning in Brazil

description: Institutional network dataset (2005-2009). (CSV 85 kb)
DOI: 10.6084/m9.figshare.c.3625979_d2.v1
title: MOESM5 of Quantitative proteomic analysis of histone modifications in decitabine sensitive and resistant leukemia cell lines

description: Additional file 5: Table S2. Relative levels of 60 PTM combinations in the different groups.
DOI: 10.6084/m9.figshare.c.3625979_d3.v1
title: MOESM1 of Quantitative proteomic analysis of histone modifications in decitabine sensitive and resistant leukemia cell lines

description: Additional file 1: Table S1. 22 histone variants and their relative levels in the different groups.
DOI: 10.6084/m9.figshare.c.3625979_d4.v1
title: MOESM2 of Quantitative proteomic analysis of histone modifications in decitabine sensitive and resistant leukemia cell lines

description: Additional file 2: Table S3. A list of 107 modified peptide species. Note: Trypsin cleaves K if propionylation is incomplete.
DOI: 10.6084/m9.figshare.c.3625994_d1.v1
title: Additional file 1: of Knowledge of complications of diabetes mellitus among patients visiting the diabetes clinic at Sampa Government Hospital, Ghana: a descriptive study

description: Data set on which conclusion of this manuscript was based upon. (XLSX 54 kb)
DOI: 10.25378/janelia.24247093
title: Manual organelle segmentations (crop136) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse liver (jrc_mus-liver)

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, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, cytosol, endosome, vesicle, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective in jrc_mus-liver 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>: crop136<br><br><b>Primary Annotator</b>: Alyson Petruncio, Nora Forknall<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>: 8 x 8 x 8 (x, y, z)<br><br><b>Annotated data dimensions (µm)</b>: 1.6 x 1.6 x 1.6 (x, y, z)<br><br><b>Annotated data offset (nm)</b>: 36504 x 28064 x 35400 (x, y, z)<br><br><b>Classes annotated</b>: mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, cytosol, endosome, vesicle, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective<br><br><b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop136<br><br><b>Source (EM) dataset ID</b>: jrc_mus-liver<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>: 101.98 x 101.82 x 71.46 (x, y, z)<br><br><b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.16913047<br><br><b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-liver<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.
DOI: 10.25378/janelia.24247093.v1
title: Manual organelle segmentations (crop136) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse liver (jrc_mus-liver)

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, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, cytosol, endosome, vesicle, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective in jrc_mus-liver 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>: crop136<br><br><b>Primary Annotator</b>: Alyson Petruncio, Nora Forknall<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>: 8 x 8 x 8 (x, y, z)<br><br><b>Annotated data dimensions (µm)</b>: 1.6 x 1.6 x 1.6 (x, y, z)<br><br><b>Annotated data offset (nm)</b>: 36504 x 28064 x 35400 (x, y, z)<br><br><b>Classes annotated</b>: mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, cytosol, endosome, vesicle, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective<br><br><b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop136<br><br><b>Source (EM) dataset ID</b>: jrc_mus-liver<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>: 101.98 x 101.82 x 71.46 (x, y, z)<br><br><b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.16913047<br><br><b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-liver<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.
DOI: 10.25378/janelia.24247087
title: Manual organelle segmentations (crop135) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse liver (jrc_mus-liver)

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, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, microtubule out, microtubule in, cytosol, endosome, vesicle, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, microtubule, cell, endoplasmic reticulum membrane collective in jrc_mus-liver 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>: crop135<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>: 8 x 8 x 8 (x, y, z)<br><br><b>Annotated data dimensions (µm)</b>: 1.6 x 1.6 x 1.6 (x, y, z)<br><br><b>Annotated data offset (nm)</b>: 54880 x 39040 x 34624 (x, y, z)<br><br><b>Classes annotated</b>: mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, microtubule out, microtubule in, cytosol, endosome, vesicle, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, microtubule, cell, endoplasmic reticulum membrane collective<br><br><b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop135<br><br><b>Source (EM) dataset ID</b>: jrc_mus-liver<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>: 101.98 x 101.82 x 71.46 (x, y, z)<br><br><b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.16913047<br><br><b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-liver<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.
DOI: 10.25378/janelia.24247087.v1
title: Manual organelle segmentations (crop135) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse liver (jrc_mus-liver)

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, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, microtubule out, microtubule in, cytosol, endosome, vesicle, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, microtubule, cell, endoplasmic reticulum membrane collective in jrc_mus-liver 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>: crop135<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>: 8 x 8 x 8 (x, y, z)<br><br><b>Annotated data dimensions (µm)</b>: 1.6 x 1.6 x 1.6 (x, y, z)<br><br><b>Annotated data offset (nm)</b>: 54880 x 39040 x 34624 (x, y, z)<br><br><b>Classes annotated</b>: mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, microtubule out, microtubule in, cytosol, endosome, vesicle, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, microtubule, cell, endoplasmic reticulum membrane collective<br><br><b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop135<br><br><b>Source (EM) dataset ID</b>: jrc_mus-liver<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>: 101.98 x 101.82 x 71.46 (x, y, z)<br><br><b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.16913047<br><br><b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-liver<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.
DOI: 10.6084/m9.figshare.c.3626120_d1.v1
title: Additional file 2: of BubbleGUM: automatic extraction of phenotype molecular signatures and comprehensive visualization of multiple Gene Set Enrichment Analyses

description: List of the transcriptomic fingerprints for murine splenic immune cell types. (XLSX 317 kb)
DOI: 10.6084/m9.figshare.c.3626114_d2.v1
title: Additional file 2: of How a concerned family member, friend or member of the public can help someone with gambling problems: a Delphi consensus study

description: Endorsed and Rejected items. (XLSX 48Â kb)
DOI: 10.25378/janelia.24247081
title: Manual organelle segmentations (crop133) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse liver (jrc_mus-liver)

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 extracellular space, plasma membrane, mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, lysosome lumen, lysosome membrane, endosome lumen, cytosol, lysosome, endosome, vesicle, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective in jrc_mus-liver 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>: crop133<br><br><b>Primary Annotator</b>: Alyson Petruncio<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>: 1.6 x 1.6 x 1.6 (x, y, z)<br><br><b>Annotated data offset (nm)</b>: 45598 x 58798 x 34198 (x, y, z)<br><br><b>Classes annotated</b>: extracellular space, plasma membrane, mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, lysosome lumen, lysosome membrane, endosome lumen, cytosol, lysosome, endosome, vesicle, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective<br><br><b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-liver/jrc_mus-liver.zarr/recon-1/labels/groundtruth/crop133<br><br><b>Source (EM) dataset ID</b>: jrc_mus-liver<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>: 101.98 x 101.82 x 71.46 (x, y, z)<br><br><b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.16913047<br><br><b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-liver<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.