fixes to pass stricter validation

bioimage-io · Feb 21, 2024 · bffb8ee · bffb8ee
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diff --git a/collection/10.5281/zenodo.5749843/resource.yaml b/collection/10.5281/zenodo.5749843/resource.yaml
@@ -6,27 +6,60 @@ 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}
+  - 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
+    weights:
+      keras_hdf5:
+        sha256: 4e34b2b630899a28f087ba607f6c8df9f32fd04240e75ee1c5ee50187070eb7c
+        source: https://zenodo.org/api/records/5888237/files/keras_model.h5/content
+        tensorflow_version: 1.15.2
+      tensorflow_saved_model_bundle:
+        parent: keras_hdf5
+        sha256: 8ae5edc5dad08a00b6c3a22e06414fd950fac751e16c7de6df60a569421b330d
+        source: https://zenodo.org/api/records/5888237/files/tensorflow_saved_model_bundle.zip/content
+        tensorflow_version: 1.15.2
+  - 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/records/5877226/files/rdf.yaml/content
+    status: blocked
+    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
diff --git a/collection/10.5281/zenodo.6079314/resource.yaml b/collection/10.5281/zenodo.6079314/resource.yaml
@@ -6,39 +6,57 @@ owners: [77626]
 status: accepted
 type: model
 versions:
-- {created: '2023-03-03 13:09:05.981223', doi: 10.5281/zenodo.7695872, name: EpitheliaAffinityModel,
-  rdf_source: 'https://zenodo.org/api/records/7695872/files/rdf.yaml/content', status: accepted,
-  version_id: '7695872', version_name: version 5}
-- {created: '2023-03-02 15:21:20.138996', doi: 10.5281/zenodo.7689587, name: EpitheliaAffinityModel,
-  rdf_source: 'https://zenodo.org/api/files/c816c201-c393-4ac4-8f68-927ee6927e23/rdf.yaml',
-  status: accepted, version_id: '7689587', version_name: version 4}
-- {created: '2023-03-01 14:17:36.817910', doi: 10.5281/zenodo.7688686, name: EpitheliaAffinityModel,
-  rdf_source: 'https://zenodo.org/api/files/e3fa2c39-d3d0-4b48-805a-76464cc93b33/rdf.yaml',
-  status: accepted, version_id: '7688686', version_name: version 3}
-- created: '2022-03-25 19:51:07.070222'
-  doi: 10.5281/zenodo.6385590
-  links: [deepimagej/deepimagej, ilastik/ilastik, imjoy/BioImageIO-Packager, ilastik/torch-em-2d-unet-notebook,
-    ilastik/mws-segmentation]
-  name: EpitheliaAffinityModel
-  rdf_source: https://zenodo.org/api/files/573e9a49-d156-46ea-838e-55ec9ebe9e00/rdf.yaml
-  status: accepted
-  version_id: '6385590'
-  version_name: version 2
-- created: '2022-02-14 17:05:09.708440'
-  doi: 10.5281/zenodo.6079315
-  inputs:
-  - axes: bcyx
-    data_range: [-.inf, .inf]
-    data_type: float32
-    name: input0
-    preprocessing:
-    - kwargs: {axes: cyx, mode: per_sample}
-      name: zero_mean_unit_variance
-    shape:
-      min: [1, 1, 48, 48]
-      step: [0, 0, 16, 16]
-  name: EpitheliaAffinityModel
-  rdf_source: https://zenodo.org/api/files/47bb6d2a-fe02-4303-9ada-12043eee17fe/rdf.yaml
-  status: accepted
-  version_id: '6079315'
-  version_name: version 1
+  - created: "2023-03-03 13:09:05.981223"
+    doi: 10.5281/zenodo.7695872
+    name: EpitheliaAffinityModel
+    rdf_source: "https://zenodo.org/api/records/7695872/files/rdf.yaml/content"
+    status: accepted
+    version_id: "7695872"
+    version_name: version 5
+  - created: "2023-03-02 15:21:20.138996"
+    doi: 10.5281/zenodo.7689587
+    name: EpitheliaAffinityModel
+    rdf_source: "https://zenodo.org/api/records/7689587/files/rdf.yaml/content"
+    status: accepted
+    version_id: "7689587"
+    version_name: version 4
+  - created: "2023-03-01 14:17:36.817910"
+    doi: 10.5281/zenodo.7688686
+    name: EpitheliaAffinityModel
+    rdf_source: "https://zenodo.org/api/records/7688686/files/rdf.yaml/content"
+    status: accepted
+    version_id: "7688686"
+    version_name: version 3
+  - created: "2022-03-25 19:51:07.070222"
+    doi: 10.5281/zenodo.6385590
+    links:
+      [
+        deepimagej/deepimagej,
+        ilastik/ilastik,
+        imjoy/BioImageIO-Packager,
+        ilastik/torch-em-2d-unet-notebook,
+        ilastik/mws-segmentation,
+      ]
+    name: EpitheliaAffinityModel
+    rdf_source: https://zenodo.org/api/records/6385590/files/rdf.yaml/content
+    status: accepted
+    version_id: "6385590"
+    version_name: version 2
+  - created: "2022-02-14 17:05:09.708440"
+    doi: 10.5281/zenodo.6079315
+    inputs:
+      - axes: bcyx
+        data_range: [-.inf, .inf]
+        data_type: float32
+        name: input0
+        preprocessing:
+          - kwargs: { axes: cyx, mode: per_sample }
+            name: zero_mean_unit_variance
+        shape:
+          min: [1, 1, 48, 48]
+          step: [0, 0, 16, 16]
+    name: EpitheliaAffinityModel
+    rdf_source: "https://zenodo.org/api/records/6079315/files/rdf.yaml/content"
+    status: accepted
+    version_id: "6079315"
+    version_name: version 1
diff --git a/collection/10.5281/zenodo.6334383/resource.yaml b/collection/10.5281/zenodo.6334383/resource.yaml
@@ -6,44 +6,90 @@ owners: [66700]
 status: accepted
 type: model
 versions:
-- {created: '2023-04-06 10:47:26.453147', doi: 10.5281/zenodo.7805067, name: 2D UNet
-    Arabidopsis Ovules, rdf_source: 'https://zenodo.org/api/records/7805067/files/rdf.yaml/content',
-  status: accepted, version_id: '7805067', version_name: version 9}
-- {created: '2023-03-29 10:46:19.177072', doi: 10.5281/zenodo.7781030, name: 2D UNet
-    Arabidopsis Ovules, rdf_source: 'https://zenodo.org/api/files/a2b1460c-40d1-4a0e-a962-9a3421470e67/rdf.yaml',
-  status: blocked, version_id: '7781030', version_name: version 8}
-- {created: '2023-03-27 00:28:36.108806', doi: 10.5281/zenodo.7772709, name: 2D UNet
-    Arabidopsis Ovules, rdf_source: 'https://zenodo.org/api/files/80145fb0-3292-4018-ac8e-e62a884d60c8/rdf.yaml',
-  status: blocked, version_id: '7772709', version_name: version 7}
-- {created: '2023-03-27 00:27:18.251839', doi: 10.5281/zenodo.7772702, name: 10.5281/zenodo.7772702,
-  rdf_source: unknown, status: blocked, version_id: '7772702', version_name: version
-    6}
-- {created: '2023-03-27 00:05:05.949230', doi: 10.5281/zenodo.7772678, name: 2D UNet
-    Arabidopsis Ovules, rdf_source: 'https://zenodo.org/api/files/d9578d83-d060-4849-8a75-c1d38253eb8c/rdf.yaml',
-  status: blocked, version_id: '7772678', version_name: version 5}
-- {created: '2023-03-06 10:21:31.082347', doi: 10.5281/zenodo.7701262, name: 2D UNet
-    Arabidopsis Ovules, rdf_source: 'https://zenodo.org/api/files/049595a1-687e-4b29-ba9e-93202322a8a1/rdf.yaml',
-  status: accepted, version_id: '7701262', version_name: version 4}
-- {created: '2023-03-03 18:42:08.763791', doi: 10.5281/zenodo.7697068, name: 2D UNet
-    Arabidopsis Ovules, rdf_source: 'https://zenodo.org/api/files/b259cb79-b631-415c-b98b-bc27cf61d4e4/rdf.yaml',
-  status: accepted, version_id: '7697068', version_name: version 3}
-- created: '2022-03-11 10:58:32.633796'
-  doi: 10.5281/zenodo.6346500
-  maintainers:
-  - {github_user: wolny}
-  name: 2D UNet Arabidopsis Ovules
-  rdf_source: https://zenodo.org/api/files/990c06ad-189d-4cfa-8168-46bb2858a634/rdf.yaml
-  status: accepted
-  version_id: '6346500'
-  version_name: version 2
-- created: '2022-03-07 11:59:05.839103'
-  doi: 10.5281/zenodo.6334384
-  maintainers:
-  - {github_user: wolny}
-  name: 2D UNet Arabidopsis Ovules
-  rdf_source: https://zenodo.org/api/files/63b44f05-a187-4fc9-81c8-c4568535531b/rdf.yaml
-  status: accepted
-  tags: [unet, 2d, semantic-segmentation, arabidopsis, ovules, cell-membrane, plant,
-    tissue, fluorescence-light-microscopy, pytorch, plantseg]
-  version_id: '6334384'
-  version_name: version 1
+  - created: "2023-04-06 10:47:26.453147"
+    doi: 10.5281/zenodo.7805067
+    name: 2D UNet
+      Arabidopsis Ovules
+    rdf_source: "https://zenodo.org/api/records/7805067/files/rdf.yaml/content"
+    status: accepted
+    version_id: "7805067"
+    version_name: version 9
+  - created: "2023-03-29 10:46:19.177072"
+    doi: 10.5281/zenodo.7781030
+    name: 2D UNet
+      Arabidopsis Ovules
+    rdf_source: "https://zenodo.org/api/files/a2b1460c-40d1-4a0e-a962-9a3421470e67/rdf.yaml"
+    status: blocked
+    version_id: "7781030"
+    version_name: version 8
+  - created: "2023-03-27 00:28:36.108806"
+    doi: 10.5281/zenodo.7772709
+    name: 2D UNet
+      Arabidopsis Ovules
+    rdf_source: "https://zenodo.org/api/files/80145fb0-3292-4018-ac8e-e62a884d60c8/rdf.yaml"
+    status: blocked
+    version_id: "7772709"
+    version_name: version 7
+  - created: "2023-03-27 00:27:18.251839"
+    doi: 10.5281/zenodo.7772702
+    name: 10.5281/zenodo.7772702
+    rdf_source: unknown
+    status: blocked
+    version_id: "7772702"
+    version_name: version 6
+  - created: "2023-03-27 00:05:05.949230"
+    doi: 10.5281/zenodo.7772678
+    name: 2D UNet
+      Arabidopsis Ovules
+    rdf_source: "https://zenodo.org/api/files/d9578d83-d060-4849-8a75-c1d38253eb8c/rdf.yaml"
+    status: blocked
+    version_id: "7772678"
+    version_name: version 5
+  - created: "2023-03-06 10:21:31.082347"
+    doi: 10.5281/zenodo.7701262
+    name: 2D UNet
+      Arabidopsis Ovules
+    rdf_source: "https://zenodo.org/api/records/7701262/files/rdf.yaml/content"
+    status: accepted
+    version_id: "7701262"
+    version_name: version 4
+  - created: "2023-03-03 18:42:08.763791"
+    doi: 10.5281/zenodo.7697068
+    name: 2D UNet
+      Arabidopsis Ovules
+    rdf_source: "https://zenodo.org/api/records/7697068/files/rdf.yaml/content"
+    status: accepted
+    version_id: "7697068"
+    version_name: version 3
+  - created: "2022-03-11 10:58:32.633796"
+    doi: 10.5281/zenodo.6346500
+    maintainers:
+      - { github_user: wolny }
+    name: 2D UNet Arabidopsis Ovules
+    rdf_source: https://zenodo.org/api/records/6346500/files/rdf.yaml/content
+    status: accepted
+    version_id: "6346500"
+    version_name: version 2
+  - created: "2022-03-07 11:59:05.839103"
+    doi: 10.5281/zenodo.6334384
+    maintainers:
+      - { github_user: wolny }
+    name: 2D UNet Arabidopsis Ovules
+    rdf_source: https://zenodo.org/api/records/6334384/files/rdf.yaml/content
+    status: accepted
+    tags:
+      [
+        unet,
+        2d,
+        semantic-segmentation,
+        arabidopsis,
+        ovules,
+        cell-membrane,
+        plant,
+        tissue,
+        fluorescence-light-microscopy,
+        pytorch,
+        plantseg,
+      ]
+    version_id: "6334384"
+    version_name: version 1
diff --git a/collection/10.5281/zenodo.6334583/resource.yaml b/collection/10.5281/zenodo.6334583/resource.yaml
@@ -6,33 +6,55 @@ owners: [66700]
 status: accepted
 type: model
 versions:
-- {created: '2023-04-06 12:43:33.436336', doi: 10.5281/zenodo.7805434, name: 3D UNet
-    Arabidopsis Ovules, rdf_source: 'https://zenodo.org/api/records/7805434/files/rdf.yaml/content',
-  status: accepted, version_id: '7805434', version_name: version 6}
-- {created: '2023-03-24 17:32:06.610900', doi: 10.5281/zenodo.7768223, name: 3D UNet
-    Arabidopsis Ovules, rdf_source: 'https://zenodo.org/api/files/e0b60143-0dc2-49e6-b62c-f2a36cf9afdc/rdf.yaml',
-  status: accepted, version_id: '7768223', version_name: version 5}
-- {created: '2023-03-06 11:08:17.979435', doi: 10.5281/zenodo.7701492, name: 3D UNet
-    Arabidopsis Ovules, rdf_source: 'https://zenodo.org/api/files/2ac87549-3ccf-4805-abd7-fac31a4bbb7c/rdf.yaml',
-  status: accepted, version_id: '7701492', version_name: version 4}
-- {created: '2023-03-03 18:24:43.192731', doi: 10.5281/zenodo.7696919, name: 3D UNet
-    Arabidopsis Ovules, rdf_source: 'https://zenodo.org/api/files/a8058f9c-ab66-4836-abcb-b1387945f39e/rdf.yaml',
-  status: accepted, version_id: '7696919', version_name: version 3}
-- created: '2022-03-11 11:06:37.200594'
-  doi: 10.5281/zenodo.6346519
-  maintainers:
-  - {github_user: wolny}
-  name: 3D UNet Arabidopsis Ovules
-  rdf_source: https://zenodo.org/api/files/9a608180-9f71-43d9-9242-b4e0a4aec21d/rdf.yaml
-  status: accepted
-  version_id: '6346519'
-  version_name: version 2
-- created: '2022-03-07 13:00:12.305646'
-  doi: 10.5281/zenodo.6334584
-  maintainers:
-  - {github_user: wolny}
-  name: 3D UNet Arabidopsis Ovules
-  rdf_source: https://zenodo.org/api/files/e1ae2d4a-a52a-4d7c-802d-892b01b263ff/rdf.yaml
-  status: accepted
-  version_id: '6334584'
-  version_name: version 1
+  - created: "2023-04-06 12:43:33.436336"
+    doi: 10.5281/zenodo.7805434
+    name: 3D UNet
+      Arabidopsis Ovules
+    rdf_source: "https://zenodo.org/api/records/7805434/files/rdf.yaml/content"
+    status: accepted
+    version_id: "7805434"
+    version_name: version 6
+  - created: "2023-03-24 17:32:06.610900"
+    doi: 10.5281/zenodo.7768223
+    name: 3D UNet
+      Arabidopsis Ovules
+    rdf_source: "https://zenodo.org/api/records/7768223/files/rdf.yaml/content"
+    status: accepted
+    version_id: "7768223"
+    version_name: version 5
+
+  - created: "2023-03-06 11:08:17.979435"
+    doi: 10.5281/zenodo.7701492
+    name: 3D UNet
+      Arabidopsis Ovules
+    rdf_source: "https://zenodo.org/api/records/7701492/files/rdf.yaml/content"
+    status: accepted
+    version_id: "7701492"
+    version_name: version 4
+
+  - created: "2023-03-03 18:24:43.192731"
+    doi: 10.5281/zenodo.7696919
+    name: 3D UNet
+      Arabidopsis Ovules
+    rdf_source: "https://zenodo.org/api/records/7696919/files/rdf.yaml/content"
+    status: accepted
+    version_id: "7696919"
+    version_name: version 3
+  - created: "2022-03-11 11:06:37.200594"
+    doi: 10.5281/zenodo.6346519
+    maintainers:
+      - { github_user: wolny }
+    name: 3D UNet Arabidopsis Ovules
+    rdf_source: "https://zenodo.org/api/records/6346519/files/rdf.yaml/content"
+    status: accepted
+    version_id: "6346519"
+    version_name: version 2
+  - created: "2022-03-07 13:00:12.305646"
+    doi: 10.5281/zenodo.6334584
+    maintainers:
+      - { github_user: wolny }
+    name: 3D UNet Arabidopsis Ovules
+    rdf_source: "https://zenodo.org/api/records/6334584/files/rdf.yaml/content"
+    status: accepted
+    version_id: "6334584"
+    version_name: version 1