cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25378/janelia.24256015
title: Manual organelle segmentations (crop208) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of (jrc_sum159-4)

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, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, cytosol, endosome, vesicle, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective in jrc_sum159-4 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>: crop208<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>: 24798 x 3678 x 21798 (x, y, z)<br><br><b>Classes annotated</b>: extracellular space, plasma membrane, mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, 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_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop208<br><br><b>Source (EM) dataset ID</b>: jrc_sum159-4<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>: 95 x 8.5 x 47.8 (x, y, z)<br><br><b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.20134103<br><br><b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_sum159-4<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.24256015.v1
title: Manual organelle segmentations (crop208) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of (jrc_sum159-4)

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, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, cytosol, endosome, vesicle, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective in jrc_sum159-4 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>: crop208<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>: 24798 x 3678 x 21798 (x, y, z)<br><br><b>Classes annotated</b>: extracellular space, plasma membrane, mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, 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_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop208<br><br><b>Source (EM) dataset ID</b>: jrc_sum159-4<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>: 95 x 8.5 x 47.8 (x, y, z)<br><br><b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.20134103<br><br><b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_sum159-4<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.3628328_d4.v1
title: Additional file 1: Table S1. of Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms

description: Raw NGS data characteristics pre and post quality filtering with Trimmomatic. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3628328_d5.v1
title: Additional file 9: Table S6. of Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms

description: p-values generated by Kolmogrov-Smirnov distribution tests. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.c.3628328_d6.v1
title: Additional file 6: Table S3. of Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms

description: Clustering metrics for the three sub-assemblies for each of the six datasets. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3628346_d4.v1
title: Additional file 4: of Variation in population levels of physical activity in European adults according to cross-European studies: a systematic literature review within DEDIPAC

description: Quality assessment file. (XLSX 14Â kb)
DOI: 10.5519/qd.9agd3nlb
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (159 records)
DOI: 10.6084/m9.figshare.c.3628328_d7.v1
title: Additional file 7: Table S4. of Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms

description: TransDecoder metrics for the concatenated assemblies for each of the six datasets. (XLSX 9Â kb)
DOI: 10.5281/zenodo.14510527
title: РАЗВИТИЕ КОММУНИКАТИВНОЙ РЕЧИ У СТУДЕНТОВ В ИНТЕРАКТИВНОЙ ОБРАЗОВАТЕЛЬНОЙ СРЕДЕ

description: Актуальность исследования заключается в необходимости поиска новых подходов и методов, способствующих эффективному развитию коммуникативной речи студентов в условиях интеграции традиционного и инновационного обучения. Рассмотрение вопроса в контексте интерактивной образовательной среды позволяет выявить потенциал современных технологий для решения данной задачи.

Целью данной статьи является анализ возможностей интерактивной образовательной среды для развития коммуникативной речи студентов, а также определение эффективных методов и приемов обучения, способствующих формированию языковой компетенции в условиях активного взаимодействия.
DOI: 10.5281/zenodo.14510528
title: РАЗВИТИЕ КОММУНИКАТИВНОЙ РЕЧИ У СТУДЕНТОВ В ИНТЕРАКТИВНОЙ ОБРАЗОВАТЕЛЬНОЙ СРЕДЕ

description: Актуальность исследования заключается в необходимости поиска новых подходов и методов, способствующих эффективному развитию коммуникативной речи студентов в условиях интеграции традиционного и инновационного обучения. Рассмотрение вопроса в контексте интерактивной образовательной среды позволяет выявить потенциал современных технологий для решения данной задачи.

Целью данной статьи является анализ возможностей интерактивной образовательной среды для развития коммуникативной речи студентов, а также определение эффективных методов и приемов обучения, способствующих формированию языковой компетенции в условиях активного взаимодействия.
DOI: 10.6084/m9.figshare.c.3628328_d8.v1
title: Additional file 2: of Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms

description: Parameter file for reads design with Flux simulator on D. melanogaster. (TXT 651 bytes)
DOI: 10.6084/m9.figshare.c.3628379_d1.v1
title: Additional file 2: of A functional genomics screen identifies an Importin-Îą homolog as a regulator of stem cell function and tissue patterning during planarian regeneration

description: Lists 1) all differentially expressed genes by gene ID with Blast2Go and KOG annotation for each gene; 2) normalized average expression levels for each gene tested in each sample type; 3) adjusted p -values for each comparison performed with differentially expressed genes highlighted in red. Where a significant change was observed, the â  expression changeâ   column provides a description of the direction of the change (up or down) and in which tissue type(s) (blastema or opposite side) the change was detected. (XLSX 1831 kb)
DOI: 10.6084/m9.figshare.c.3628328_d9.v1
title: Additional file 4: of Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms

description: Perl script used to randomly select candidates from a list of transcripts for our PCR validation experiments. (PL 10Â kb)
DOI: 10.25378/janelia.24256021
title: Manual organelle segmentations (crop210) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of (jrc_sum159-4)

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, 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_sum159-4 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>: crop210<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>: 1.6 x 1.6 x 1.6 (x, y, z)<br><br><b>Annotated data offset (nm)</b>: 26462 x 3806 x 15134 (x, y, z)<br><br><b>Classes annotated</b>: extracellular space, plasma membrane, mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, 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_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop210<br><br><b>Source (EM) dataset ID</b>: jrc_sum159-4<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>: 95 x 8.5 x 47.8 (x, y, z)<br><br><b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.20134103<br><br><b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_sum159-4<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.24256021.v1
title: Manual organelle segmentations (crop210) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of (jrc_sum159-4)

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, 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_sum159-4 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>: crop210<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>: 1.6 x 1.6 x 1.6 (x, y, z)<br><br><b>Annotated data offset (nm)</b>: 26462 x 3806 x 15134 (x, y, z)<br><br><b>Classes annotated</b>: extracellular space, plasma membrane, mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, 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_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop210<br><br><b>Source (EM) dataset ID</b>: jrc_sum159-4<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>: 95 x 8.5 x 47.8 (x, y, z)<br><br><b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.20134103<br><br><b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_sum159-4<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.3628481_d2.v1
title: Additional file 4: Table S4. of Epigenomic and metabolic responses of hypothalamic POMC neurons to gestational nicotine exposure in adult offspring

description: Co-expressed lncRNAs and protein-coding genes in cis. Co-expression of lncRNAs (columns A and B) with their nearest (adjacent or overlapping) protein-coding gene (column D) was determined by the Pearson’s correlation coefficient r (column F). An r value &gt; 0.602 or  1 CPM (columns K and L) were considered for analyses. LncRNA expression was in most cases less than that of the coding gene (column M). Coding genes function in various biological processes (column N). (XLSX 63 kb)
DOI: 10.6084/m9.figshare.c.3628475_d3.v1
title: Additional file 2: of Genomic and functional analyses unveil the response to hyphal wall stress in Candida albicans cells lacking Î˛(1,3)-glucan remodeling

description: Class 1: Transcripts that are more abundant in the phr1Î  mutant than in the wild type. (XLSX 45 kb)
DOI: 10.6084/m9.figshare.c.3628454_d7.v1
title: Additional file 11: Table S10. of 
                     Andrographis paniculata transcriptome provides molecular insights into tissue-specific accumulation of medicinal diterpenes

description: SSRs in leaf transcripts. (XLS 2660 kb)
DOI: 10.6084/m9.figshare.c.3628481_d3.v1
title: Additional file 2: Table S2. of Epigenomic and metabolic responses of hypothalamic POMC neurons to gestational nicotine exposure in adult offspring

description: Expressed protein-coding genes in PANTHER pathways. Expressed protein-coding genes denoted by Ensembl Gene ID (column A), gene name and symbol (column B), Panther family/subfamily (column C), Panther protein class (column D), and average expression in CPM (column E) were assigned to PANTHER defined pathways, which are referred to by name and accession number. Only genes expressed at levelsâ  &gt;â  1 CPM were considered for analysis. CPM counts per million. (XLSX 172 kb)
DOI: 10.6084/m9.figshare.c.3628481_d4.v1
title: Additional file 3: Table S3. of Epigenomic and metabolic responses of hypothalamic POMC neurons to gestational nicotine exposure in adult offspring

description: Expression ranking of lncRNAs in POMC neurons. LncRNA genes referred to by Ensembl Gene ID (column A), gene name (column B), and gene type (column C) were ranked by average expression across all samples (column D). Only lncRNA genes expressed at levelsâ  &gt;â  1 CPM were considered for analysis. CPM counts per million. (XLSX 98 kb)
DOI: 10.6084/m9.figshare.c.3628454_d8.v1
title: Additional file 9: Table S8. of 
                     Andrographis paniculata transcriptome provides molecular insights into tissue-specific accumulation of medicinal diterpenes

description: Putative transcription factors. (XLSX 45 kb)
DOI: 10.25378/janelia.24256024
title: Manual organelle segmentations (crop211) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of (jrc_sum159-4)

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 nucleus, mitochondria in jrc_sum159-4 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>: crop211<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>: 8 x 8 x 8 (x, y, z)<br><br><b>Annotated data dimensions (µm)</b>: 6.4 x 6.4 x 6.4 (x, y, z)<br><br><b>Annotated data offset (nm)</b>: 31008 x 1760 x 27504 (x, y, z)<br><br><b>Classes annotated</b>: nucleus, mitochondria<br><br><b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop211<br><br><b>Source (EM) dataset ID</b>: jrc_sum159-4<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>: 95 x 8.5 x 47.8 (x, y, z)<br><br><b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.20134103<br><br><b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_sum159-4<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.24256024.v1
title: Manual organelle segmentations (crop211) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of (jrc_sum159-4)

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 nucleus, mitochondria in jrc_sum159-4 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>: crop211<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>: 8 x 8 x 8 (x, y, z)<br><br><b>Annotated data dimensions (µm)</b>: 6.4 x 6.4 x 6.4 (x, y, z)<br><br><b>Annotated data offset (nm)</b>: 31008 x 1760 x 27504 (x, y, z)<br><br><b>Classes annotated</b>: nucleus, mitochondria<br><br><b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_sum159-4/jrc_sum159-4.zarr/recon-1/labels/groundtruth/crop211<br><br><b>Source (EM) dataset ID</b>: jrc_sum159-4<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>: 95 x 8.5 x 47.8 (x, y, z)<br><br><b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.20134103<br><br><b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_sum159-4<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.