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FynnBe · Dec 13, 2023 · e5df2c6 · e5df2c6
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diff --git a/partner_collection/fiji/N2VSEMDemo/resource.yaml b/partner_collection/fiji/N2VSEMDemo/resource.yaml
@@ -1,114 +1,2 @@
 id: fiji/N2VSEMDemo
-status: accepted
-type: model
-versions:
-- name: N2V SEM Demo
-  status: accepted
-  version_id: latest
-  version_name: latest
-  rdf_source:
-    authors:
-    - affiliation: MDC Berlin
-      name: Deborah Schmidt
-    cite:
-    - doi: https://doi.org/10.1016/bs.mch.2019.05.001
-      text: Buchholz, T. et al. - Content-aware image restoration for electron microscopy.
-        Methods in Cell Biology, Volume 152 p.277-289, ISSN 0091-679X (2019)
-    config:
-      fiji:
-        batchDimLength: 180
-        batchSize: 64
-        neighborhoodRadius: 5
-        numEpochs: 100
-        numStepsPerEpoch: 300
-        patchDimLength: 60
-        stepsFinished: 30000
-        trainDimensions: 2
-    covers:
-    - https://raw.githubusercontent.com/bioimage-io/fiji-bioimage-io/master/models/n2v-sem-demo/thumbnail.png
-    description: Demo model for denoising trained on a single SEM image with Noise2Void
-    documentation: 
-      https://raw.githubusercontent.com/bioimage-io/fiji-bioimage-io/master/models/n2v-sem-demo/README.md
-    format_version: 0.3.6
-    framework: tensorflow
-    id: fiji/N2VSEMDemo
-    inputs:
-    - axes: byxc
-      data_range:
-      - -.inf
-      - .inf
-      data_type: float32
-      name: input
-      preprocessing:
-      - kwargs:
-          axes: ycx
-          mean: 41498.87
-          mode: fixed
-          std: 15007.021
-        name: zero_mean_unit_variance
-      shape:
-        min:
-        - 1
-        - 68
-        - 68
-        - 1
-        step:
-        - 0
-        - 4
-        - 4
-        - 0
-    language: java
-    license: BSD-3-Clause
-    links:
-    - fiji/Fiji
-    name: N2V SEM Demo
-    outputs:
-    - axes: byxc
-      data_range:
-      - -.inf
-      - .inf
-      data_type: float32
-      halo:
-      - 0
-      - 32
-      - 32
-      - 0
-      name: denoised
-      postprocessing:
-      - kwargs:
-          axes: ycx
-          gain: 41498.87
-          offset: 15007.021
-        name: scale_linear
-      shape:
-        offset:
-        - 0.0
-        - 0.0
-        - 0.0
-        - 0.0
-        reference_tensor: input
-        scale:
-        - 1.0
-        - 1.0
-        - 1.0
-        - 1.0
-    tags:
-    - denoising
-    - unet2d
-    - n2v
-    test_inputs:
-    - https://raw.githubusercontent.com/bioimage-io/fiji-bioimage-io/master/models/n2v-sem-demo/test_input.tif
-    test_outputs:
-    - https://raw.githubusercontent.com/bioimage-io/fiji-bioimage-io/master/models/n2v-sem-demo/test_output.tif
-    timestamp: '2021-06-03T13:34:19.685956'
-    type: model
-    version: 0.1.2
-    weights:
-      tensorflow_saved_model_bundle:
-        authors:
-        - affiliation: MDC Berlin
-          name: Deborah Schmidt
-        sha256: c55ab5528ec0dd8b3e00062df155ba00aef4971d7eacc3ed2d41db1f25917994
-        source: 
-          https://github.com/bioimage-io/fiji-bioimage-io/releases/download/v0.3.1/n2v-sem-demo_savedmodelbundle.zip
-        tensorflow_version: 1.13.1
+status: deleted
diff --git a/partner_collection/ilastik/arabidopsis_tissue_atlas/resource.yaml b/partner_collection/ilastik/arabidopsis_tissue_atlas/resource.yaml
@@ -26,6 +26,7 @@ versions:
       splash_title: ilastik
       tags:
       - ilastik
+      - software
       url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
     covers:
     - https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main/dataset_src/arabidopsis_atlas.jpg

diff --git a/partner_collection/ilastik/covid_if_training_data/resource.yaml b/partner_collection/ilastik/covid_if_training_data/resource.yaml
@@ -29,6 +29,7 @@ versions:
       splash_title: ilastik
       tags:
       - ilastik
+      - software
       url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
     covers:
     - https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main/dataset_src/covid-if-cover0.jpg

diff --git a/partner_collection/ilastik/cremi_training_data/resource.yaml b/partner_collection/ilastik/cremi_training_data/resource.yaml
@@ -30,6 +30,7 @@ versions:
       splash_title: ilastik
       tags:
       - ilastik
+      - software
       url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
     covers:
     - https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main/dataset_src/cremi-cover0.png

diff --git a/partner_collection/ilastik/ilastik/resource.yaml b/partner_collection/ilastik/ilastik/resource.yaml
@@ -31,6 +31,7 @@ versions:
       splash_title: ilastik
       tags:
       - ilastik
+      - software
       url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
     covers: []
     description: the interactive learning and segmentation toolkit

diff --git a/partner_collection/ilastik/isbi2012_neuron_segmentation_challenge/resource.yaml b/partner_collection/ilastik/isbi2012_neuron_segmentation_challenge/resource.yaml
@@ -29,6 +29,7 @@ versions:
       splash_title: ilastik
       tags:
       - ilastik
+      - software
       url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
     covers:
     - https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main/dataset_src/isbi2012-cover0.jpg

diff --git a/partner_collection/ilastik/livecell_dataset/resource.yaml b/partner_collection/ilastik/livecell_dataset/resource.yaml
@@ -29,6 +29,7 @@ versions:
       splash_title: ilastik
       tags:
       - ilastik
+      - software
       url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
     covers:
     - https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main/dataset_src/livecell-cover0.jpg

diff --git a/partner_collection/ilastik/mitoem_segmentation_challenge/resource.yaml b/partner_collection/ilastik/mitoem_segmentation_challenge/resource.yaml
@@ -29,6 +29,7 @@ versions:
       splash_title: ilastik
       tags:
       - ilastik
+      - software
       url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
     covers:
     - https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main/dataset_src/mitoem-cover0.jpg

diff --git a/partner_collection/ilastik/mws-segmentation/resource.yaml b/partner_collection/ilastik/mws-segmentation/resource.yaml
@@ -31,6 +31,7 @@ versions:
       splash_title: ilastik
       tags:
       - ilastik
+      - software
       url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
     covers: []
     description: Segmentation plugin for models that predict pixel affinities

diff --git a/partner_collection/ilastik/plantseg_ovules/resource.yaml b/partner_collection/ilastik/plantseg_ovules/resource.yaml
@@ -29,6 +29,7 @@ versions:
       splash_title: ilastik
       tags:
       - ilastik
+      - software
       url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
     covers:
     - https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main/dataset_src/plantseg_cover.jpg

diff --git a/partner_collection/ilastik/plantseg_root/resource.yaml b/partner_collection/ilastik/plantseg_root/resource.yaml
@@ -29,6 +29,7 @@ versions:
       splash_title: ilastik
       tags:
       - ilastik
+      - software
       url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
     covers:
     - https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main/dataset_src/plantseg_cover.jpg

diff --git a/partner_collection/ilastik/platynereis_em_training_data/resource.yaml b/partner_collection/ilastik/platynereis_em_training_data/resource.yaml
@@ -29,6 +29,7 @@ versions:
       splash_title: ilastik
       tags:
       - ilastik
+      - software
       url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
     covers:
     - https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main/dataset_src/platy-cover0.png

diff --git a/partner_collection/ilastik/stardist_dsb_training_data/resource.yaml b/partner_collection/ilastik/stardist_dsb_training_data/resource.yaml
@@ -29,6 +29,7 @@ versions:
       splash_title: ilastik
       tags:
       - ilastik
+      - software
       url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
     covers:
     - https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main/dataset_src/dsb-cover0.jpg

diff --git a/partner_collection/ilastik/tnbc/resource.yaml b/partner_collection/ilastik/tnbc/resource.yaml
@@ -29,6 +29,7 @@ versions:
       splash_title: ilastik
       tags:
       - ilastik
+      - software
       url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
     covers:
     - https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main/dataset_src/tnbc_cover.jpg

diff --git a/partner_collection/ilastik/torch-em-2d-unet-notebook/resource.yaml b/partner_collection/ilastik/torch-em-2d-unet-notebook/resource.yaml
@@ -29,6 +29,7 @@ versions:
       splash_title: ilastik
       tags:
       - ilastik
+      - software
       url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
     covers:
     - https://raw.githubusercontent.com/constantinpape/torch-em/main/experiments/misc/targets.png

diff --git a/partner_collection/ilastik/torch-em-3d-unet-notebook/resource.yaml b/partner_collection/ilastik/torch-em-3d-unet-notebook/resource.yaml
@@ -29,6 +29,7 @@ versions:
       splash_title: ilastik
       tags:
       - ilastik
+      - software
       url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
     covers:
     - https://raw.githubusercontent.com/constantinpape/torch-em/main/experiments/misc/targets.png

diff --git a/partner_collection/ilastik/vnc/resource.yaml b/partner_collection/ilastik/vnc/resource.yaml
@@ -29,6 +29,7 @@ versions:
       splash_title: ilastik
       tags:
       - ilastik
+      - software
       url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
     covers:
     - https://s3-eu-west-1.amazonaws.com/pfigshare-u-previews/1288336/preview.jpg

diff --git a/partner_collection_hashes.json b/partner_collection_hashes.json
@@ -2,12 +2,12 @@
   "bioimageio": "f549651922eba99405e291b42bfb3440ad466670",
   "bioimageio_spec_version": "0.4.9post4",
   "deepimagej": "b4131c47b805c09896119a661ca13c968614ae8a",
-  "fiji": "4c94a8ca7052b155a1265b20827a44b7fcc4835c",
+  "fiji": "55c67f6d27a21a0b17fd65306b04ea7e34e9dd05",
   "hpa": "8b166c0fc23cfa5f06de838cab07b4651a546951",
   "icy": "ffa9fb4d5ed89317a0f126bc9a416f62451cf3d8",
-  "ilastik": "c173addab8c5423f3eb4aa4e2cdac2442c240132",
+  "ilastik": "63acedc7eb0299730367249d0253b0f938d01e19",
   "imjoy": "f8f594dd4ff89210549e96e1949d34728852ba18",
   "qupath": "d1c9f00e2dc05c340cf8b6f7c1d8d10773f0ccfc",
   "stardist": "b5bf5043a07eda17dd23acf969f18e9a64d8962c",
-  "zero": "1afc3938a7706eda0a741e289fa4efbadd4859a7"
+  "zero": "728412e727425827ccb1760cc05ddd49ef7a3e7b"
 }
diff --git a/partner_details.json b/partner_details.json
@@ -202,7 +202,8 @@
         "splash_subtitle": "the interactive learning and segmentation toolkit",
         "splash_title": "ilastik",
         "tags": [
-            "ilastik"
+            "ilastik",
+            "software"
         ],
         "test_summaries": {
             "deploy_branch": "gh-pages",

diff --git a/rdfs/ilastik/arabidopsis_tissue_atlas/latest/rdf.yaml b/rdfs/ilastik/arabidopsis_tissue_atlas/latest/rdf.yaml
@@ -21,6 +21,7 @@ config:
   splash_title: ilastik
   tags:
   - ilastik
+  - software
   url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
 covers:
 - https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main/dataset_src/arabidopsis_atlas.jpg

diff --git a/rdfs/ilastik/covid_if_training_data/latest/rdf.yaml b/rdfs/ilastik/covid_if_training_data/latest/rdf.yaml
@@ -24,6 +24,7 @@ config:
   splash_title: ilastik
   tags:
   - ilastik
+  - software
   url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
 covers:
 - https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main/dataset_src/covid-if-cover0.jpg

diff --git a/rdfs/ilastik/cremi_training_data/latest/rdf.yaml b/rdfs/ilastik/cremi_training_data/latest/rdf.yaml
@@ -24,6 +24,7 @@ config:
   splash_title: ilastik
   tags:
   - ilastik
+  - software
   url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
 covers:
 - https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main/dataset_src/cremi-cover0.png

diff --git a/rdfs/ilastik/ilastik/latest/rdf.yaml b/rdfs/ilastik/ilastik/latest/rdf.yaml
@@ -26,6 +26,7 @@ config:
   splash_title: ilastik
   tags:
   - ilastik
+  - software
   url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
 covers: []
 description: the interactive learning and segmentation toolkit

diff --git a/rdfs/ilastik/isbi2012_neuron_segmentation_challenge/latest/rdf.yaml b/rdfs/ilastik/isbi2012_neuron_segmentation_challenge/latest/rdf.yaml
@@ -24,6 +24,7 @@ config:
   splash_title: ilastik
   tags:
   - ilastik
+  - software
   url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
 covers:
 - https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main/dataset_src/isbi2012-cover0.jpg

diff --git a/rdfs/ilastik/livecell_dataset/latest/rdf.yaml b/rdfs/ilastik/livecell_dataset/latest/rdf.yaml
@@ -24,6 +24,7 @@ config:
   splash_title: ilastik
   tags:
   - ilastik
+  - software
   url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
 covers:
 - https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main/dataset_src/livecell-cover0.jpg

diff --git a/rdfs/ilastik/mitoem_segmentation_challenge/latest/rdf.yaml b/rdfs/ilastik/mitoem_segmentation_challenge/latest/rdf.yaml
@@ -24,6 +24,7 @@ config:
   splash_title: ilastik
   tags:
   - ilastik
+  - software
   url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
 covers:
 - https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main/dataset_src/mitoem-cover0.jpg

diff --git a/rdfs/ilastik/mws-segmentation/latest/rdf.yaml b/rdfs/ilastik/mws-segmentation/latest/rdf.yaml
@@ -25,6 +25,7 @@ config:
   splash_title: ilastik
   tags:
   - ilastik
+  - software
   url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
 covers: []
 description: Segmentation plugin for models that predict pixel affinities

diff --git a/rdfs/ilastik/plantseg_ovules/latest/rdf.yaml b/rdfs/ilastik/plantseg_ovules/latest/rdf.yaml
@@ -24,6 +24,7 @@ config:
   splash_title: ilastik
   tags:
   - ilastik
+  - software
   url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
 covers:
 - https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main/dataset_src/plantseg_cover.jpg

diff --git a/rdfs/ilastik/plantseg_root/latest/rdf.yaml b/rdfs/ilastik/plantseg_root/latest/rdf.yaml
@@ -24,6 +24,7 @@ config:
   splash_title: ilastik
   tags:
   - ilastik
+  - software
   url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
 covers:
 - https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main/dataset_src/plantseg_cover.jpg

diff --git a/rdfs/ilastik/platynereis_em_training_data/latest/rdf.yaml b/rdfs/ilastik/platynereis_em_training_data/latest/rdf.yaml
@@ -24,6 +24,7 @@ config:
   splash_title: ilastik
   tags:
   - ilastik
+  - software
   url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
 covers:
 - https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main/dataset_src/platy-cover0.png

diff --git a/rdfs/ilastik/stardist_dsb_training_data/latest/rdf.yaml b/rdfs/ilastik/stardist_dsb_training_data/latest/rdf.yaml
@@ -24,6 +24,7 @@ config:
   splash_title: ilastik
   tags:
   - ilastik
+  - software
   url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
 covers:
 - https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main/dataset_src/dsb-cover0.jpg

diff --git a/rdfs/ilastik/tnbc/latest/rdf.yaml b/rdfs/ilastik/tnbc/latest/rdf.yaml
@@ -24,6 +24,7 @@ config:
   splash_title: ilastik
   tags:
   - ilastik
+  - software
   url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
 covers:
 - https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main/dataset_src/tnbc_cover.jpg

diff --git a/rdfs/ilastik/torch-em-2d-unet-notebook/latest/rdf.yaml b/rdfs/ilastik/torch-em-2d-unet-notebook/latest/rdf.yaml
@@ -24,6 +24,7 @@ config:
   splash_title: ilastik
   tags:
   - ilastik
+  - software
   url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
 covers:
 - https://raw.githubusercontent.com/constantinpape/torch-em/main/experiments/misc/targets.png

diff --git a/rdfs/ilastik/torch-em-3d-unet-notebook/latest/rdf.yaml b/rdfs/ilastik/torch-em-3d-unet-notebook/latest/rdf.yaml
@@ -24,6 +24,7 @@ config:
   splash_title: ilastik
   tags:
   - ilastik
+  - software
   url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
 covers:
 - https://raw.githubusercontent.com/constantinpape/torch-em/main/experiments/misc/targets.png

diff --git a/rdfs/ilastik/vnc/latest/rdf.yaml b/rdfs/ilastik/vnc/latest/rdf.yaml
@@ -24,6 +24,7 @@ config:
   splash_title: ilastik
   tags:
   - ilastik
+  - software
   url_root: https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main
 covers:
 - https://s3-eu-west-1.amazonaws.com/pfigshare-u-previews/1288336/preview.jpg