Merge pull request #654 from bioimage-io/zenodo_update

update zenodo.org/api calls

Author: FynnBe

collection/10.5281/zenodo.5744489/resource.yaml

@@ -1,10 +1,10 @@
-doi: 10.5281/zenodo.5744489
-id: 10.5281/zenodo.5744489
-status: blocked
-type: model
-versions:
-- {created: '2021-12-25 18:54:04.735769', doi: 10.5281/zenodo.5744490, name: UNet
-    2D Nuclei Broad, rdf_source: 'https://zenodo.org/api/files/3f422e1b-a64e-40d3-89d1-29038d2f405d/rdf.yaml',
-  status: blocked, version_id: '5744490', version_name: revision 1}
-nickname: communicative-dolphin
-nickname_icon: 🐬
+doi: 10.5281/zenodo.5744489
+id: 10.5281/zenodo.5744489
+nickname: communicative-dolphin
+nickname_icon: "\U0001F42C"
+status: blocked
+type: model
+versions:
+- {created: '2021-12-25 18:54:04.735769', doi: 10.5281/zenodo.5744490, name: UNet
+    2D Nuclei Broad, rdf_source: 'https://zenodo.org/api/records/5744490/files/rdf.yaml/content',
+  status: blocked, version_id: '5744490', version_name: revision 1}

collection/10.5281/zenodo.5749843/resource.yaml

@@ -1,35 +1,32 @@
-doi: 10.5281/zenodo.5749843
-id: 10.5281/zenodo.5749843
-owners: [252845]
-status: accepted
-type: model
-versions:
-- created: '2022-01-21 14:50:48.356997'
-  doi: 10.5281/zenodo.5888237
-  name: 'Cell Segmentation from Membrane Staining for Plant Tissues'
-  rdf_source: 'https://zenodo.org/api/files/eb8f4259-001c-4989-b8ea-d2997918599d/rdf.yaml'
-  status: accepted
-  version_id: '5888237'
-  version_name: revision 1
-  links: [imjoy/BioImageIO-Packager, ilastik/ilastik, deepimagej/deepimagej, zero/notebook_u-net_3d_zerocostdl4mic]
-  tags: [zerocostdl4mic, deepimagej, segmentation, 3d, unet, fluorescence-light-microscopy, cell-membrane, plant, arabidopsis, tensorflow]
-  training_data:
-    id: ilastik/plantseg_ovules
-  description: 'A 3D U-net to predict cell membranes in plant tissues, trained on volumes of Arabidopsis thaliana ovules acquired on a confocal microscope.'
-- created: '2022-01-19 10:16:02.455027'
-  doi: 10.5281/zenodo.5877226
-  name: '3D UNet - arabidopsis - ZeroCostDL4Mic'
-  rdf_source: 'https://zenodo.org/api/files/3759664b-38bf-4ba8-b61d-b017dcf420d1/rdf.yaml'
-  status: accepted
-  version_id: '5877226'
-  version_name: revision 2
-  links: [imjoy/BioImageIO-Packager, ilastik/ilastik, deepimagej/deepimagej]
-- created: '2021-12-02 14:27:16.753974+00:00'
-  doi: 10.5281/zenodo.5749844
-  name: '3D UNet - arabidopsis - ZeroCostDL4Mic'
-  rdf_source: 'https://zenodo.org/api/files/3320859e-af1a-45bc-bfaa-3d4110b3bc41/rdf.yaml'
-  status: blocked
-  version_id: '5749844'
-  version_name: revision 1
-nickname: humorous-owl
-nickname_icon: 🦉
+doi: 10.5281/zenodo.5749843
+id: 10.5281/zenodo.5749843
+nickname: humorous-owl
+nickname_icon: "\U0001F989"
+owners: [252845]
+status: accepted
+type: model
+versions:
+- created: '2022-01-21 14:50:48.356997'
+  description: A 3D U-net to predict cell membranes in plant tissues, trained on volumes
+    of Arabidopsis thaliana ovules acquired on a confocal microscope.
+  doi: 10.5281/zenodo.5888237
+  links: [imjoy/BioImageIO-Packager, ilastik/ilastik, deepimagej/deepimagej, zero/notebook_u-net_3d_zerocostdl4mic]
+  name: Cell Segmentation from Membrane Staining for Plant Tissues
+  rdf_source: https://zenodo.org/api/records/5888237/files/rdf.yaml/content
+  status: accepted
+  tags: [zerocostdl4mic, deepimagej, segmentation, 3d, unet, fluorescence-light-microscopy,
+    cell-membrane, plant, arabidopsis, tensorflow]
+  training_data: {id: ilastik/plantseg_ovules}
+  version_id: '5888237'
+  version_name: revision 1
+- created: '2022-01-19 10:16:02.455027'
+  doi: 10.5281/zenodo.5877226
+  links: [imjoy/BioImageIO-Packager, ilastik/ilastik, deepimagej/deepimagej]
+  name: 3D UNet - arabidopsis - ZeroCostDL4Mic
+  rdf_source: https://zenodo.org/api/files/3759664b-38bf-4ba8-b61d-b017dcf420d1/rdf.yaml
+  status: accepted
+  version_id: '5877226'
+  version_name: revision 2
+- {created: '2021-12-02 14:27:16.753974+00:00', doi: 10.5281/zenodo.5749844, name: 3D
+    UNet - arabidopsis - ZeroCostDL4Mic, rdf_source: 'https://zenodo.org/api/files/3320859e-af1a-45bc-bfaa-3d4110b3bc41/rdf.yaml',
+  status: blocked, version_id: '5749844', version_name: revision 1}

collection/10.5281/zenodo.5764892/resource.yaml

@@ -1,65 +1,35 @@
-doi: 10.5281/zenodo.5764892
-id: 10.5281/zenodo.5764892
-nickname: affable-shark
-nickname_icon: 🦈
-owners:
-- 77626
-status: accepted
-type: model
-versions:
-- created: '2022-06-15 22:06:22.658325'
-  doi: 10.5281/zenodo.6647674
-  name: NucleiSegmentationBoundaryModel
-  status: accepted
-  version_id: '6647674'
-  version_name: version 7
-  rdf_source: https://zenodo.org/api/files/61da5c68-e09b-49a6-899b-94c22cdfc4d9/rdf.yaml
-- created: '2022-03-02 12:07:39.352008'
-  doi: 10.5281/zenodo.6322939
-  links:
-  - deepimagej/deepimagej
-  - ilastik/ilastik
-  - imjoy/BioImageIO-Packager
-  - ilastik/torch-em-2d-unet-notebook
-  name: NucleiSegmentationBoundaryModel
-  status: accepted
-  training_data:
-    id: ilastik/stardist_dsb_training_data
-  version_id: '6322939'
-  version_name: revision 1
-  rdf_source: https://zenodo.org/api/files/a3d790f1-5203-4bd3-a975-d0fff38c0d97/rdf.yaml
-- created: '2022-03-01 09:27:03.758432'
-  doi: 10.5281/zenodo.6319663
-  name: NucleiSegmentationBoundaryModel
-  status: blocked
-  version_id: '6319663'
-  version_name: revision 2
-  rdf_source: https://zenodo.org/api/files/1cf7ce1f-f1a1-4207-9e3e-60ee4d4a0803/rdf.yaml
-- created: '2022-02-25 20:18:26.146167'
-  doi: 10.5281/zenodo.6287342
-  name: NucleiSegmentationBoundaryModel
-  status: blocked
-  version_id: '6287342'
-  version_name: revision 3
-  rdf_source: https://zenodo.org/api/files/0f39fc4f-e8ea-4af5-be7d-e756b566c09f/rdf.yaml
-- created: '2022-02-25 20:10:17.778295'
-  doi: 10.5281/zenodo.6287207
-  name: NucleiSegmentationBoundaryModel
-  status: blocked
-  version_id: '6287207'
-  version_name: revision 4
-  rdf_source: https://zenodo.org/api/files/7d930716-b8c4-4a23-922c-91e561d237b7/rdf.yaml
-- created: '2022-02-09 20:56:44.509499'
-  doi: 10.5281/zenodo.6028056
-  name: NucleiSegmentationBoundaryModel
-  status: blocked
-  version_id: '6028056'
-  version_name: revision 5
-  rdf_source: https://zenodo.org/api/files/50a4c576-db4c-49a6-a691-59f9d96e6d5f/rdf.yaml
-- created: '2021-12-07 18:02:09.736653+00:00'
-  doi: 10.5281/zenodo.5764893
-  name: NucleiSegmentationBoundaryModel
-  status: blocked
-  version_id: '5764893'
-  version_name: revision 1
-  rdf_source: https://zenodo.org/api/files/8137780b-871f-4d7e-b130-a63847ece4d8/rdf.yaml
+doi: 10.5281/zenodo.5764892
+id: 10.5281/zenodo.5764892
+nickname: affable-shark
+nickname_icon: "\U0001F988"
+owners: [77626]
+status: accepted
+type: model
+versions:
+- {created: '2022-06-15 22:06:22.658325', doi: 10.5281/zenodo.6647674, name: NucleiSegmentationBoundaryModel,
+  rdf_source: 'https://zenodo.org/api/records/6647674/files/rdf.yaml/content', status: accepted,
+  version_id: '6647674', version_name: version 7}
+- created: '2022-03-02 12:07:39.352008'
+  doi: 10.5281/zenodo.6322939
+  links: [deepimagej/deepimagej, ilastik/ilastik, imjoy/BioImageIO-Packager, ilastik/torch-em-2d-unet-notebook]
+  name: NucleiSegmentationBoundaryModel
+  rdf_source: https://zenodo.org/api/files/a3d790f1-5203-4bd3-a975-d0fff38c0d97/rdf.yaml
+  status: accepted
+  training_data: {id: ilastik/stardist_dsb_training_data}
+  version_id: '6322939'
+  version_name: revision 1
+- {created: '2022-03-01 09:27:03.758432', doi: 10.5281/zenodo.6319663, name: NucleiSegmentationBoundaryModel,
+  rdf_source: 'https://zenodo.org/api/files/1cf7ce1f-f1a1-4207-9e3e-60ee4d4a0803/rdf.yaml',
+  status: blocked, version_id: '6319663', version_name: revision 2}
+- {created: '2022-02-25 20:18:26.146167', doi: 10.5281/zenodo.6287342, name: NucleiSegmentationBoundaryModel,
+  rdf_source: 'https://zenodo.org/api/files/0f39fc4f-e8ea-4af5-be7d-e756b566c09f/rdf.yaml',
+  status: blocked, version_id: '6287342', version_name: revision 3}
+- {created: '2022-02-25 20:10:17.778295', doi: 10.5281/zenodo.6287207, name: NucleiSegmentationBoundaryModel,
+  rdf_source: 'https://zenodo.org/api/files/7d930716-b8c4-4a23-922c-91e561d237b7/rdf.yaml',
+  status: blocked, version_id: '6287207', version_name: revision 4}
+- {created: '2022-02-09 20:56:44.509499', doi: 10.5281/zenodo.6028056, name: NucleiSegmentationBoundaryModel,
+  rdf_source: 'https://zenodo.org/api/files/50a4c576-db4c-49a6-a691-59f9d96e6d5f/rdf.yaml',
+  status: blocked, version_id: '6028056', version_name: revision 5}
+- {created: '2021-12-07 18:02:09.736653+00:00', doi: 10.5281/zenodo.5764893, name: NucleiSegmentationBoundaryModel,
+  rdf_source: 'https://zenodo.org/api/files/8137780b-871f-4d7e-b130-a63847ece4d8/rdf.yaml',
+  status: blocked, version_id: '5764893', version_name: revision 1}

collection/10.5281/zenodo.5817052/resource.yaml

@@ -1,17 +1,23 @@
-doi: 10.5281/zenodo.5817052
-id: 10.5281/zenodo.5817052
-owners: [271523]
-status: accepted
-type: model
-versions:
-- {created: '2022-01-27 14:00:17.489637', doi: 10.5281/zenodo.5906839, name: Neuron Segmentation in 2D EM (Membrane), rdf_source: 'https://zenodo.org/api/files/5a9cfb56-3a5d-4796-986d-8f46b7987b92/rdf.yaml',
-  tags: [zerocostdl4mic, deepimagej, segmentation, electron-microscopy, unet, isbi2012-challenge, neurons, brain,
-  boundary-segmentation, 2d], status: accepted, version_id: '5906839', version_name: revision 1}
-- {created: '2022-01-14 15:26:42.112259', doi: 10.5281/zenodo.5850574, name: Mitochondria
-    segmentation - TEM - 2D U-Net - ZeroCostDL4Mic, rdf_source: 'https://zenodo.org/api/files/5ff5e52c-a708-4c93-98c2-160c29204800/rdf.yaml',
-  status: accepted, version_id: '5850574', version_name: revision 1}
-- {created: '2022-01-04 11:33:05.251713', doi: 10.5281/zenodo.5817053, name: Mitochondria
-    segmentation - TEM - 2D U-Net - ZeroCostDL4Mic, rdf_source: 'https://zenodo.org/api/files/e14f65fa-f480-4503-944a-209e3119b38b/rdf.yaml',
-  status: blocked, version_id: '5817053', version_name: revision 1}
-nickname: creative-panda
-nickname_icon: 🐼
+doi: 10.5281/zenodo.5817052
+id: 10.5281/zenodo.5817052
+nickname: creative-panda
+nickname_icon: "\U0001F43C"
+owners: [271523]
+status: accepted
+type: model
+versions:
+- created: '2022-01-27 14:00:17.489637'
+  doi: 10.5281/zenodo.5906839
+  name: Neuron Segmentation in 2D EM (Membrane)
+  rdf_source: https://zenodo.org/api/records/5906839/files/rdf.yaml/content
+  status: accepted
+  tags: [zerocostdl4mic, deepimagej, segmentation, electron-microscopy, unet, isbi2012-challenge,
+    neurons, brain, boundary-segmentation, 2d]
+  version_id: '5906839'
+  version_name: revision 1
+- {created: '2022-01-14 15:26:42.112259', doi: 10.5281/zenodo.5850574, name: Mitochondria
+    segmentation - TEM - 2D U-Net - ZeroCostDL4Mic, rdf_source: 'https://zenodo.org/api/files/5ff5e52c-a708-4c93-98c2-160c29204800/rdf.yaml',
+  status: accepted, version_id: '5850574', version_name: revision 1}
+- {created: '2022-01-04 11:33:05.251713', doi: 10.5281/zenodo.5817053, name: Mitochondria
+    segmentation - TEM - 2D U-Net - ZeroCostDL4Mic, rdf_source: 'https://zenodo.org/api/files/e14f65fa-f480-4503-944a-209e3119b38b/rdf.yaml',
+  status: blocked, version_id: '5817053', version_name: revision 1}

collection/10.5281/zenodo.5847355/resource.yaml

@@ -1,44 +1,26 @@
-doi: 10.5281/zenodo.5847355
-id: 10.5281/zenodo.5847355
-nickname: powerful-chipmunk
-nickname_icon: 🐿
-owners:
-- 77626
-status: accepted
-type: model
-versions:
-- created: '2022-06-15 22:08:13.874556'
-  doi: 10.5281/zenodo.6647683
-  name: CovidIFCellSegmentationBoundaryModel
-  status: accepted
-  version_id: '6647683'
-  version_name: version 4
-  rdf_source: https://zenodo.org/api/files/67864f33-063b-43e9-a40f-0f36bf6397d4/rdf.yaml
-- created: '2022-03-02 11:57:10.309729'
-  doi: 10.5281/zenodo.6322908
-  links:
-  - deepimagej/deepimagej
-  - ilastik/ilastik
-  - imjoy/BioImageIO-Packager
-  - ilastik/torch-em-2d-unet-notebook
-  name: CovidIFCellSegmentationBoundaryModel
-  status: accepted
-  training_data:
-    id: ilastik/covid_if_training_data
-  version_id: '6322908'
-  version_name: revision 1
-  rdf_source: https://zenodo.org/api/files/be41e515-ce79-48f5-a482-35e1f11701c2/rdf.yaml
-- created: '2022-01-18 21:31:33.668428'
-  doi: 10.5281/zenodo.5874728
-  name: Cell Segmentation Immunofluorescence (Membrane Prediction)
-  status: blocked
-  version_id: '5874728'
-  version_name: revision 1
-  rdf_source: https://zenodo.org/api/files/612ad5b1-5978-4481-9c8c-e28b97d6b927/rdf.yaml
-- created: '2022-01-13 21:13:49.264581'
-  doi: 10.5281/zenodo.5847356
-  name: CovidIFCellSegmentationBoundaryModel
-  status: blocked
-  version_id: '5847356'
-  version_name: revision 1
-  rdf_source: https://zenodo.org/api/files/5b0d4c67-6d0a-462c-914c-07bebe594bd8/rdf.yaml
+doi: 10.5281/zenodo.5847355
+id: 10.5281/zenodo.5847355
+nickname: powerful-chipmunk
+nickname_icon: "\U0001F43F"
+owners: [77626]
+status: accepted
+type: model
+versions:
+- {created: '2022-06-15 22:08:13.874556', doi: 10.5281/zenodo.6647683, name: CovidIFCellSegmentationBoundaryModel,
+  rdf_source: 'https://zenodo.org/api/records/6647683/files/rdf.yaml/content', status: accepted,
+  version_id: '6647683', version_name: version 4}
+- created: '2022-03-02 11:57:10.309729'
+  doi: 10.5281/zenodo.6322908
+  links: [deepimagej/deepimagej, ilastik/ilastik, imjoy/BioImageIO-Packager, ilastik/torch-em-2d-unet-notebook]
+  name: CovidIFCellSegmentationBoundaryModel
+  rdf_source: https://zenodo.org/api/files/be41e515-ce79-48f5-a482-35e1f11701c2/rdf.yaml
+  status: accepted
+  training_data: {id: ilastik/covid_if_training_data}
+  version_id: '6322908'
+  version_name: revision 1
+- {created: '2022-01-18 21:31:33.668428', doi: 10.5281/zenodo.5874728, name: Cell
+    Segmentation Immunofluorescence (Membrane Prediction), rdf_source: 'https://zenodo.org/api/files/612ad5b1-5978-4481-9c8c-e28b97d6b927/rdf.yaml',
+  status: blocked, version_id: '5874728', version_name: revision 1}
+- {created: '2022-01-13 21:13:49.264581', doi: 10.5281/zenodo.5847356, name: CovidIFCellSegmentationBoundaryModel,
+  rdf_source: 'https://zenodo.org/api/files/5b0d4c67-6d0a-462c-914c-07bebe594bd8/rdf.yaml',
+  status: blocked, version_id: '5847356', version_name: revision 1}

collection/10.5281/zenodo.5869899/resource.yaml

@@ -1,43 +1,29 @@
-doi: 10.5281/zenodo.5869899
-id: 10.5281/zenodo.5869899
-nickname: hiding-tiger
-nickname_icon: 🐅
-owners:
-- 77626
-status: accepted
-type: model
-versions:
-- created: '2022-06-15 22:09:35.368273'
-  doi: 10.5281/zenodo.6647688
-  name: LiveCellSegmentationBoundaryModel
-  status: accepted
-  version_id: '6647688'
-  version_name: version 3
-  rdf_source: https://zenodo.org/api/files/8e1dc6e7-bdc9-412c-b06c-e79ee375989f/rdf.yaml
-- created: '2022-03-01 19:53:40.554063'
-  doi: 10.5281/zenodo.6321179
-  links:
-  - deepimagej/deepimagej
-  - ilastik/ilastik
-  - imjoy/BioImageIO-Packager
-  - ilastik/torch-em-2d-unet-notebook
-  name: LiveCellSegmentationBoundaryModel
-  status: accepted
-  training_data:
-    id: ilastik/livecell_dataset
-  version_id: '6321179'
-  version_name: revision 1
-  rdf_source: https://zenodo.org/api/files/f2a796dc-27f5-43b8-aadb-981898f39b87/rdf.yaml
-- created: '2022-01-18 10:03:26.939252'
-  doi: 10.5281/zenodo.5869900
-  links:
-  - ilastik/live-cell-boundary-model
-  - ilastik/livecell_dataset
-  - ilastik/ilastik
-  - deepimagej/deepimagej
-  - imjoy/BioImageIO-Packager
-  name: LiveCellSegmentationBoundaryModel
-  status: accepted
-  version_id: '5869900'
-  version_name: revision 1
-  rdf_source: https://zenodo.org/api/files/a6d477fe-9412-4064-b7e6-67f057fec920/rdf.yaml
+doi: 10.5281/zenodo.5869899
+id: 10.5281/zenodo.5869899
+nickname: hiding-tiger
+nickname_icon: "\U0001F405"
+owners: [77626]
+status: accepted
+type: model
+versions:
+- {created: '2022-06-15 22:09:35.368273', doi: 10.5281/zenodo.6647688, name: LiveCellSegmentationBoundaryModel,
+  rdf_source: 'https://zenodo.org/api/records/6647688/files/rdf.yaml/content', status: accepted,
+  version_id: '6647688', version_name: version 3}
+- created: '2022-03-01 19:53:40.554063'
+  doi: 10.5281/zenodo.6321179
+  links: [deepimagej/deepimagej, ilastik/ilastik, imjoy/BioImageIO-Packager, ilastik/torch-em-2d-unet-notebook]
+  name: LiveCellSegmentationBoundaryModel
+  rdf_source: https://zenodo.org/api/files/f2a796dc-27f5-43b8-aadb-981898f39b87/rdf.yaml
+  status: accepted
+  training_data: {id: ilastik/livecell_dataset}
+  version_id: '6321179'
+  version_name: revision 1
+- created: '2022-01-18 10:03:26.939252'
+  doi: 10.5281/zenodo.5869900
+  links: [ilastik/live-cell-boundary-model, ilastik/livecell_dataset, ilastik/ilastik,
+    deepimagej/deepimagej, imjoy/BioImageIO-Packager]
+  name: LiveCellSegmentationBoundaryModel
+  rdf_source: https://zenodo.org/api/files/a6d477fe-9412-4064-b7e6-67f057fec920/rdf.yaml
+  status: accepted
+  version_id: '5869900'
+  version_name: revision 1