cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3621887_d3.v1
title: Additional file 2: of Putative synaptic genes defined from a Drosophila whole body developmental transcriptome by a machine learning approach

description: List of non-synaptic genes. A .csv file listing the 397 “non-synaptic” genes. (CSV 10 kb)
DOI: 10.6084/m9.figshare.c.3621887_d4.v1
title: Additional file 5: of Putative synaptic genes defined from a Drosophila whole body developmental transcriptome by a machine learning approach

description: List of genes with tissue-specific differential expression. A.csv file with the list of genes that show tissue-specific differential expression in the five selected tissues as described in Methods. (CSV 30ย�kb)
DOI: 10.6084/m9.figshare.c.3621890_d2.v1
title: Additional file 1: of KIR repertory in patients with hematopoietic diseases and healthy family members

description: Patients – Supporting Information. (XLS 43 kb)
DOI: 10.6084/m9.figshare.c.3621887_d5.v1
title: Additional file 1: of Putative synaptic genes defined from a Drosophila whole body developmental transcriptome by a machine learning approach

description: List of synaptic genes and references. A .csv file listing the 92 genes labeled as “synaptic genes” and the corresponding bibliographic references. (CSV 25 kb)
DOI: 10.25378/janelia.24260857
title: Manual organelle segmentations (crop274) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse liver acinus (jrc_mus-liver-zon-1)

description: <b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<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, lysosome lumen, lysosome membrane, endosome lumen, cytosol, lysosome, endosome, vesicle, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective 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.<b>Annotation ID</b>: crop274<b>Primary Annotator</b>: Alyson Petruncio<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)<b>Software</b>: Amira 3D 2021.1, Classic Segmentation Workroom<b>Annotated voxel size (nm)</b>: 4 x 4 x 4 (x, y, z)<b>Annotated data dimensions (µm)</b>: 1.6 x 1.6 x 1.6 (x, y, z)<b>Annotated data offset (nm)</b>: 76798 x 48398 x 95470 (x, y, z)<b>Classes annotated</b>: 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<b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop274<b>Source (EM) dataset ID</b>: jrc_mus-liver-zon-1<b>Source (EM) voxel size (nm)</b>: 8 x 8 x 8 (x, y, z)<b>Source (EM) data dimensions (µm)</b>: 397.16 x 171.61 x 188.81 (x, y, z)<b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.24128700<b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-liver-zon-1<b>Publication:</b> <i>CellMap Segmentation Challenge,</i> 2024.<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.<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.24260857.v1
title: Manual organelle segmentations (crop274) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse liver acinus (jrc_mus-liver-zon-1)

description: <b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<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, lysosome lumen, lysosome membrane, endosome lumen, cytosol, lysosome, endosome, vesicle, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective 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.<b>Annotation ID</b>: crop274<b>Primary Annotator</b>: Alyson Petruncio<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)<b>Software</b>: Amira 3D 2021.1, Classic Segmentation Workroom<b>Annotated voxel size (nm)</b>: 4 x 4 x 4 (x, y, z)<b>Annotated data dimensions (µm)</b>: 1.6 x 1.6 x 1.6 (x, y, z)<b>Annotated data offset (nm)</b>: 76798 x 48398 x 95470 (x, y, z)<b>Classes annotated</b>: 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<b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop274<b>Source (EM) dataset ID</b>: jrc_mus-liver-zon-1<b>Source (EM) voxel size (nm)</b>: 8 x 8 x 8 (x, y, z)<b>Source (EM) data dimensions (µm)</b>: 397.16 x 171.61 x 188.81 (x, y, z)<b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.24128700<b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-liver-zon-1<b>Publication:</b> <i>CellMap Segmentation Challenge,</i> 2024.<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.<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.3621887_d8.v1
title: Additional file 6: of Putative synaptic genes defined from a Drosophila whole body developmental transcriptome by a machine learning approach

description: Putative catalogue of synaptic genes. A .csv file with the final catalogue of 893 Drosophila genes that according to the three algorithms have a probability above 90 % of being involved in synapse assembly and function. (CSV 35 kb)
DOI: 10.6084/m9.figshare.c.3622082_d16.v1
title: Additional file 5: Table S5. of Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data

description: List of samples used for the 1-nearest-neighbour analysis for supra-species classification and their respective taxonomic ranks. (XLS 29Â kb)
DOI: 10.6084/m9.figshare.c.3622160_d4.v1
title: Additional file 6: of The idiopathic preterm delivery methylation profile in umbilical cord blood DNA

description: Systematic differences (DMPs) Initiation with spontaneous PtLb vs PPROM. (XLS 44Â kb)
DOI: 10.6084/m9.figshare.c.3622172_d1.v1
title: Additional file 5: Table S3. of Characterization of VHL missense mutations in sporadic clear cell renal cell carcinoma: hotspots, affected binding domains, functional impact on pVHL and therapeutic relevance

description: List of missense mutations, stability and disease association prediction. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.c.3622160_d5.v1
title: Additional file 1: of The idiopathic preterm delivery methylation profile in umbilical cord blood DNA

description: Patient data. (XLS 104Â kb)
DOI: 10.6084/m9.figshare.c.3622160_d6.v1
title: Additional file 2: of The idiopathic preterm delivery methylation profile in umbilical cord blood DNA

description: DMPs correlating to gestational age (refers to Fig.Â  3c ). (XLSX 140Â kb)
DOI: 10.6084/m9.figshare.c.3622184_d1.v1
title: Additional file 1: of Differential fall migratory routes of adult and juvenile Ipswich Sparrows (Passerculus sandwichensis princeps)

description: Receiver station locations and antenna orientations. Start and Stop times refer to the period each receiver was active. Some changes in antenna orientation occurred (eg. CANS1 & CANS2) however sites remained active during orientation changes and therefore were unlikely to impact detections during this study. Receivers were maintained and checked for operation on a cycle of weeks or months depending on site accessibility. Evaluation of raw data showed no major receiver malfunctions except at 3 locations, all of which should not have affected data: CANS1 was non-operational for 3 days (Nov 10–13) however CANS2 was within 1 km and was operational during this time; KEJI was non-operational for 8 days (between Nov 8–19) however only one individual was detected for the first time after Nov 8th and it was first detected 150 km NE at CONRD, thus this likely did not affect overwater flight information from Sable Island to the mainland; STAGE had frequent blackouts however LOT1 was within 5 km. (XLS 37 kb)
DOI: 10.6084/m9.figshare.c.3622160_d7.v1
title: Additional file 5: of The idiopathic preterm delivery methylation profile in umbilical cord blood DNA

description: a. Systematic differences (DMPs) Oxcytocin use. b. Oxcytocin use-wikipathways. (ZIP 25Â kb)
DOI: 10.6084/m9.figshare.c.3622178_d3.v1
title: Additional file 11: of Transcriptome profile analysis of cell proliferation molecular processes during multicellular trichome formation induced by tomato Wo
                     v gene in tobacco

description: The list of all KEGG pathways of the differentially expressed genes. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.c.3622181_d3.v1
title: Additional file 3: Table S2. of Intracellular Ca2+ and K+ concentration in Brassica oleracea leaf induces differential expression of transporter and stress-related genes

description: Expression levels of significant changed genes. (XLSX 2520 kb)
DOI: 10.6084/m9.figshare.c.3622172_d3.v1
title: Additional file 3: Table S2. of Characterization of VHL missense mutations in sporadic clear cell renal cell carcinoma: hotspots, affected binding domains, functional impact on pVHL and therapeutic relevance

description: List of all VHL mutations. (XLSX 21Â kb)
DOI: 10.6084/m9.figshare.c.3622178_d4.v1
title: Additional file 9: of Transcriptome profile analysis of cell proliferation molecular processes during multicellular trichome formation induced by tomato Wo
                     v gene in tobacco

description: Expression patterns of the homologues of the known trichome-related genes in transgenic tobacco plants. (XLS 28Â kb)
DOI: 10.25378/janelia.24260851
title: Manual organelle segmentations (crop273) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse liver acinus (jrc_mus-liver-zon-1)

description: <b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<b>Annotation description</b>: Dense segmentations of mitochondrial membrane, mitochondrial lumen, endosome membrane, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, lysosome lumen, lysosome membrane, endosome lumen, cytosol, lysosome, endosome, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective 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.<b>Annotation ID</b>: crop273<b>Primary Annotator</b>: Diana Ramirez<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)<b>Software</b>: Amira 3D 2021.1, Classic Segmentation Workroom<b>Annotated voxel size (nm)</b>: 4 x 4 x 4 (x, y, z)<b>Annotated data dimensions (µm)</b>: 1.6 x 1.6 x 1.6 (x, y, z)<b>Annotated data offset (nm)</b>: 65254 x 60574 x 195334 (x, y, z)<b>Classes annotated</b>: mitochondrial membrane, mitochondrial lumen, endosome membrane, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, lysosome lumen, lysosome membrane, endosome lumen, cytosol, lysosome, endosome, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective<b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop273<b>Source (EM) dataset ID</b>: jrc_mus-liver-zon-1<b>Source (EM) voxel size (nm)</b>: 8 x 8 x 8 (x, y, z)<b>Source (EM) data dimensions (µm)</b>: 397.16 x 171.61 x 188.81 (x, y, z)<b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.24128700<b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-liver-zon-1<b>Publication:</b> <i>CellMap Segmentation Challenge,</i> 2024.<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.<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.24260851.v1
title: Manual organelle segmentations (crop273) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse liver acinus (jrc_mus-liver-zon-1)

description: <b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<b>Annotation description</b>: Dense segmentations of mitochondrial membrane, mitochondrial lumen, endosome membrane, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, lysosome lumen, lysosome membrane, endosome lumen, cytosol, lysosome, endosome, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective 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.<b>Annotation ID</b>: crop273<b>Primary Annotator</b>: Diana Ramirez<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)<b>Software</b>: Amira 3D 2021.1, Classic Segmentation Workroom<b>Annotated voxel size (nm)</b>: 4 x 4 x 4 (x, y, z)<b>Annotated data dimensions (µm)</b>: 1.6 x 1.6 x 1.6 (x, y, z)<b>Annotated data offset (nm)</b>: 65254 x 60574 x 195334 (x, y, z)<b>Classes annotated</b>: mitochondrial membrane, mitochondrial lumen, endosome membrane, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, lysosome lumen, lysosome membrane, endosome lumen, cytosol, lysosome, endosome, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective<b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop273<b>Source (EM) dataset ID</b>: jrc_mus-liver-zon-1<b>Source (EM) voxel size (nm)</b>: 8 x 8 x 8 (x, y, z)<b>Source (EM) data dimensions (µm)</b>: 397.16 x 171.61 x 188.81 (x, y, z)<b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.24128700<b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-liver-zon-1<b>Publication:</b> <i>CellMap Segmentation Challenge,</i> 2024.<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.<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.3622178_d5.v1
title: Additional file 10: of Transcriptome profile analysis of cell proliferation molecular processes during multicellular trichome formation induced by tomato Wo
                     v gene in tobacco

description: Differentially expressed transcription factors found in the Wo v transgenic tobacco plants compared with its wild type. (XLS 34Â kb)
DOI: 10.6084/m9.figshare.c.3622355_d6.v1
title: Additional file 2: Table S2. of A proteomic analysis of chondrogenic, osteogenic and tenogenic constructs from ageing mesenchymal stem cells

description: Presenting details of the antibodies used for validation studies. (XLSX 10 kb)
DOI: 10.25378/janelia.24260839
title: Manual organelle segmentations (crop272) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse liver acinus (jrc_mus-liver-zon-1)

description: <b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<b>Annotation description</b>: Dense segmentations of mitochondrial membrane, mitochondrial lumen, vesicle membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, cytosol, vesicle, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective 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.<b>Annotation ID</b>: crop272<b>Primary Annotator</b>: Woohyun Park<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)<b>Software</b>: Amira 3D 2021.1, Classic Segmentation Workroom<b>Annotated voxel size (nm)</b>: 4 x 4 x 4 (x, y, z)<b>Annotated data dimensions (µm)</b>: 1.6 x 1.6 x 1.6 (x, y, z)<b>Annotated data offset (nm)</b>: 158710 x 56886 x 197198 (x, y, z)<b>Classes annotated</b>: mitochondrial membrane, mitochondrial lumen, vesicle membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, cytosol, vesicle, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective<br><br><b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop272<b>Source (EM) dataset ID</b>: jrc_mus-liver-zon-1<b>Source (EM) voxel size (nm)</b>: 8 x 8 x 8 (x, y, z)<b>Source (EM) data dimensions (µm)</b>: 397.16 x 171.61 x 188.81 (x, y, z)<b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.24128700<b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-liver-zon-1<b>Publication:</b> <i>CellMap Segmentation Challenge,</i> 2024.<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.<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.24260839.v1
title: Manual organelle segmentations (crop272) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse liver acinus (jrc_mus-liver-zon-1)

description: <b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<b>Annotation description</b>: Dense segmentations of mitochondrial membrane, mitochondrial lumen, vesicle membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, cytosol, vesicle, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective 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.<b>Annotation ID</b>: crop272<b>Primary Annotator</b>: Woohyun Park<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)<b>Software</b>: Amira 3D 2021.1, Classic Segmentation Workroom<b>Annotated voxel size (nm)</b>: 4 x 4 x 4 (x, y, z)<b>Annotated data dimensions (µm)</b>: 1.6 x 1.6 x 1.6 (x, y, z)<b>Annotated data offset (nm)</b>: 158710 x 56886 x 197198 (x, y, z)<b>Classes annotated</b>: mitochondrial membrane, mitochondrial lumen, vesicle membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, cytosol, vesicle, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective<br><br><b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop272<b>Source (EM) dataset ID</b>: jrc_mus-liver-zon-1<b>Source (EM) voxel size (nm)</b>: 8 x 8 x 8 (x, y, z)<b>Source (EM) data dimensions (µm)</b>: 397.16 x 171.61 x 188.81 (x, y, z)<b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.24128700<b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-liver-zon-1<b>Publication:</b> <i>CellMap Segmentation Challenge,</i> 2024.<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.<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.3622355_d7.v1
title: Additional file 3: Table S3. of A proteomic analysis of chondrogenic, osteogenic and tenogenic constructs from ageing mesenchymal stem cells

description: Presenting the proteins identified in PEAKS PTM using the human reviewed database. (XLSX 425 kb)