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FynnBe · Sep 13, 2023 · 22c97a3 · 22c97a3
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diff --git a/collection.json b/collection.json
@@ -65,7 +65,7 @@
         "https://zenodo.org/api/files/334f9dd9-ae1e-46e2-9a6a-5445758c4e9c/cover.png"
       ],
       "description": "{organelle} segmentation in EM of platynereis.",
-      "download_count": 29804,
+      "download_count": 29859,
       "id": "10.5281/zenodo.6028097",
       "license": "CC-BY-4.0",
       "links": [
@@ -296,7 +296,7 @@
         "https://zenodo.org/api/files/0e7404c7-daad-4a1f-9fa8-f12aaa7842cb/cover.png"
       ],
       "description": "Prediction enhancer for segmenting mitochondria in EM images.",
-      "download_count": 14391,
+      "download_count": 14439,
       "id": "10.5281/zenodo.6811491",
       "license": "CC-BY-4.0",
       "links": [
@@ -524,45 +524,6 @@
         "6028281"
       ]
     },
-    {
-      "authors": [
-        {
-          "name": "Constantin Pape"
-        }
-      ],
-      "covers": [
-        "https://zenodo.org/api/files/ac8ecde9-bafd-4c2c-9ede-0f4a47077d31/cover.png"
-      ],
-      "description": "Mitochondria segmentation for electron microscopy.",
-      "download_count": 9260,
-      "id": "10.5281/zenodo.5874841",
-      "license": "CC-BY-4.0",
-      "links": [
-        "deepimagej/deepimagej",
-        "ilastik/ilastik",
-        "ilastik/mitoem_segmentation_challenge",
-        "imjoy/BioImageIO-Packager"
-      ],
-      "name": "MitochondriaEMSegmentationBoundaryModel",
-      "nickname": "kind-seashell",
-      "nickname_icon": "\ud83d\udc1a",
-      "owners": [
-        77626
-      ],
-      "rdf_source": "https://FynnBe.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.5874841/6630266/rdf.yaml",
-      "tags": [
-        "3d",
-        "electron-microscopy",
-        "mitochondria",
-        "instance-segmentation",
-        "unet"
-      ],
-      "type": "model",
-      "versions": [
-        "6630266",
-        "5874842"
-      ]
-    },
     {
       "authors": [
         {
@@ -578,7 +539,7 @@
         "https://zenodo.org/api/files/4a1f1eaf-685f-4564-810a-25e1e268b3e5/pred-nuclei.png"
       ],
       "description": "A 3D U-Net trained to predict the nuclei and their boundaries in fixed confocal images of developing mouse embryo.Voxel size: (0.2\u00d70.2\u00d71 \u00b5m^3) (XYZ).",
-      "download_count": 9244,
+      "download_count": 9261,
       "id": "10.5281/zenodo.6383429",
       "license": "MIT",
       "links": [
@@ -609,6 +570,45 @@
         "6383430"
       ]
     },
+    {
+      "authors": [
+        {
+          "name": "Constantin Pape"
+        }
+      ],
+      "covers": [
+        "https://zenodo.org/api/files/ac8ecde9-bafd-4c2c-9ede-0f4a47077d31/cover.png"
+      ],
+      "description": "Mitochondria segmentation for electron microscopy.",
+      "download_count": 9260,
+      "id": "10.5281/zenodo.5874841",
+      "license": "CC-BY-4.0",
+      "links": [
+        "deepimagej/deepimagej",
+        "ilastik/ilastik",
+        "ilastik/mitoem_segmentation_challenge",
+        "imjoy/BioImageIO-Packager"
+      ],
+      "name": "MitochondriaEMSegmentationBoundaryModel",
+      "nickname": "kind-seashell",
+      "nickname_icon": "\ud83d\udc1a",
+      "owners": [
+        77626
+      ],
+      "rdf_source": "https://FynnBe.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.5874841/6630266/rdf.yaml",
+      "tags": [
+        "3d",
+        "electron-microscopy",
+        "mitochondria",
+        "instance-segmentation",
+        "unet"
+      ],
+      "type": "model",
+      "versions": [
+        "6630266",
+        "5874842"
+      ]
+    },
     {
       "authors": [
         {
@@ -622,7 +622,7 @@
         "https://zenodo.org/api/files/858dbb84-174e-48cb-b2ef-9f1db2d0b275/hpaseg-cover.png"
       ],
       "description": "Cell segmentation model for segmenting images from the Human Protein Atlas",
-      "download_count": 6571,
+      "download_count": 6597,
       "id": "10.5281/zenodo.6200635",
       "license": "CC-BY-4.0",
       "links": [
@@ -1325,7 +1325,7 @@
         "https://zenodo.org/api/files/0c6f4346-c936-420b-89be-322f6df574ae/hpaseg-cover.png"
       ],
       "description": "Nuclei segmentation model for segmenting images from the Human Protein Atlas",
-      "download_count": 3076,
+      "download_count": 3091,
       "id": "10.5281/zenodo.6200999",
       "license": "CC-BY-4.0",
       "links": [
@@ -1364,7 +1364,7 @@
         "https://zenodo.org/api/files/5a9cfb56-3a5d-4796-986d-8f46b7987b92/cover.png"
       ],
       "description": "2D UNet trained using ZeroCostDL4Mic notebooks on data from ISBI Challenge for neuron segmentation in Transmission Electron Microscopy images.",
-      "download_count": 3061,
+      "download_count": 3076,
       "id": "10.5281/zenodo.5817052",
       "license": "MIT",
       "links": [

diff --git a/rdf.json b/rdf.json
@@ -65,7 +65,7 @@
         "https://zenodo.org/api/files/334f9dd9-ae1e-46e2-9a6a-5445758c4e9c/cover.png"
       ],
       "description": "{organelle} segmentation in EM of platynereis.",
-      "download_count": 29804,
+      "download_count": 29859,
       "id": "10.5281/zenodo.6028097",
       "license": "CC-BY-4.0",
       "links": [
@@ -296,7 +296,7 @@
         "https://zenodo.org/api/files/0e7404c7-daad-4a1f-9fa8-f12aaa7842cb/cover.png"
       ],
       "description": "Prediction enhancer for segmenting mitochondria in EM images.",
-      "download_count": 14391,
+      "download_count": 14439,
       "id": "10.5281/zenodo.6811491",
       "license": "CC-BY-4.0",
       "links": [
@@ -524,45 +524,6 @@
         "6028281"
       ]
     },
-    {
-      "authors": [
-        {
-          "name": "Constantin Pape"
-        }
-      ],
-      "covers": [
-        "https://zenodo.org/api/files/ac8ecde9-bafd-4c2c-9ede-0f4a47077d31/cover.png"
-      ],
-      "description": "Mitochondria segmentation for electron microscopy.",
-      "download_count": 9260,
-      "id": "10.5281/zenodo.5874841",
-      "license": "CC-BY-4.0",
-      "links": [
-        "deepimagej/deepimagej",
-        "ilastik/ilastik",
-        "ilastik/mitoem_segmentation_challenge",
-        "imjoy/BioImageIO-Packager"
-      ],
-      "name": "MitochondriaEMSegmentationBoundaryModel",
-      "nickname": "kind-seashell",
-      "nickname_icon": "\ud83d\udc1a",
-      "owners": [
-        77626
-      ],
-      "rdf_source": "https://FynnBe.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.5874841/6630266/rdf.yaml",
-      "tags": [
-        "3d",
-        "electron-microscopy",
-        "mitochondria",
-        "instance-segmentation",
-        "unet"
-      ],
-      "type": "model",
-      "versions": [
-        "6630266",
-        "5874842"
-      ]
-    },
     {
       "authors": [
         {
@@ -578,7 +539,7 @@
         "https://zenodo.org/api/files/4a1f1eaf-685f-4564-810a-25e1e268b3e5/pred-nuclei.png"
       ],
       "description": "A 3D U-Net trained to predict the nuclei and their boundaries in fixed confocal images of developing mouse embryo.Voxel size: (0.2\u00d70.2\u00d71 \u00b5m^3) (XYZ).",
-      "download_count": 9244,
+      "download_count": 9261,
       "id": "10.5281/zenodo.6383429",
       "license": "MIT",
       "links": [
@@ -609,6 +570,45 @@
         "6383430"
       ]
     },
+    {
+      "authors": [
+        {
+          "name": "Constantin Pape"
+        }
+      ],
+      "covers": [
+        "https://zenodo.org/api/files/ac8ecde9-bafd-4c2c-9ede-0f4a47077d31/cover.png"
+      ],
+      "description": "Mitochondria segmentation for electron microscopy.",
+      "download_count": 9260,
+      "id": "10.5281/zenodo.5874841",
+      "license": "CC-BY-4.0",
+      "links": [
+        "deepimagej/deepimagej",
+        "ilastik/ilastik",
+        "ilastik/mitoem_segmentation_challenge",
+        "imjoy/BioImageIO-Packager"
+      ],
+      "name": "MitochondriaEMSegmentationBoundaryModel",
+      "nickname": "kind-seashell",
+      "nickname_icon": "\ud83d\udc1a",
+      "owners": [
+        77626
+      ],
+      "rdf_source": "https://FynnBe.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.5874841/6630266/rdf.yaml",
+      "tags": [
+        "3d",
+        "electron-microscopy",
+        "mitochondria",
+        "instance-segmentation",
+        "unet"
+      ],
+      "type": "model",
+      "versions": [
+        "6630266",
+        "5874842"
+      ]
+    },
     {
       "authors": [
         {
@@ -622,7 +622,7 @@
         "https://zenodo.org/api/files/858dbb84-174e-48cb-b2ef-9f1db2d0b275/hpaseg-cover.png"
       ],
       "description": "Cell segmentation model for segmenting images from the Human Protein Atlas",
-      "download_count": 6571,
+      "download_count": 6597,
       "id": "10.5281/zenodo.6200635",
       "license": "CC-BY-4.0",
       "links": [
@@ -1325,7 +1325,7 @@
         "https://zenodo.org/api/files/0c6f4346-c936-420b-89be-322f6df574ae/hpaseg-cover.png"
       ],
       "description": "Nuclei segmentation model for segmenting images from the Human Protein Atlas",
-      "download_count": 3076,
+      "download_count": 3091,
       "id": "10.5281/zenodo.6200999",
       "license": "CC-BY-4.0",
       "links": [
@@ -1364,7 +1364,7 @@
         "https://zenodo.org/api/files/5a9cfb56-3a5d-4796-986d-8f46b7987b92/cover.png"
       ],
       "description": "2D UNet trained using ZeroCostDL4Mic notebooks on data from ISBI Challenge for neuron segmentation in Transmission Electron Microscopy images.",
-      "download_count": 3061,
+      "download_count": 3076,
       "id": "10.5281/zenodo.5817052",
       "license": "MIT",
       "links": [

diff --git a/rdf.yaml b/rdf.yaml
@@ -25,7 +25,7 @@ collection:
   - {name: Constantin Pape; @constantinpape}
   covers: ['https://zenodo.org/api/files/334f9dd9-ae1e-46e2-9a6a-5445758c4e9c/cover.png']
   description: '{organelle} segmentation in EM of platynereis.'
-  download_count: 29804
+  download_count: 29859
   id: 10.5281/zenodo.6028097
   license: CC-BY-4.0
   links: [deepimagej/deepimagej, ilastik/ilastik, imjoy/BioImageIO-Packager, ilastik/torch-em-3d-unet-notebook]
@@ -117,7 +117,7 @@ collection:
   - {affiliation: EMBL Heidelberg, name: Constantin Pape}
   covers: ['https://zenodo.org/api/files/0e7404c7-daad-4a1f-9fa8-f12aaa7842cb/cover.png']
   description: Prediction enhancer for segmenting mitochondria in EM images.
-  download_count: 14391
+  download_count: 14439
   id: 10.5281/zenodo.6811491
   license: CC-BY-4.0
   links: [deepimagej/deepimagej, ilastik/torch-em-3d-unet-notebook, ilastik/ilastik,
@@ -215,23 +215,6 @@ collection:
   tags: [unet, cells, instance-segmentation, electron-microscopy, platynereis]
   type: model
   versions: ['6647695', '6028281']
-- authors:
-  - {name: Constantin Pape}
-  covers: ['https://zenodo.org/api/files/ac8ecde9-bafd-4c2c-9ede-0f4a47077d31/cover.png']
-  description: Mitochondria segmentation for electron microscopy.
-  download_count: 9260
-  id: 10.5281/zenodo.5874841
-  license: CC-BY-4.0
-  links: [deepimagej/deepimagej, ilastik/ilastik, ilastik/mitoem_segmentation_challenge,
-    imjoy/BioImageIO-Packager]
-  name: MitochondriaEMSegmentationBoundaryModel
-  nickname: kind-seashell
-  nickname_icon: "\U0001F41A"
-  owners: [77626]
-  rdf_source: https://FynnBe.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.5874841/6630266/rdf.yaml
-  tags: [3d, electron-microscopy, mitochondria, instance-segmentation, unet]
-  type: model
-  versions: ['6630266', '5874842']
 - authors:
   - {name: V. Bondarenko}
   - {name: A. Wolny}
@@ -240,7 +223,7 @@ collection:
     'https://zenodo.org/api/files/4a1f1eaf-685f-4564-810a-25e1e268b3e5/pred-nuclei.png']
   description: 'A 3D U-Net trained to predict the nuclei and their boundaries in fixed
     confocal images of developing mouse embryo.Voxel size: (0.2×0.2×1 µm^3) (XYZ).'
-  download_count: 9244
+  download_count: 9261
   id: 10.5281/zenodo.6383429
   license: MIT
   links: [imjoy/BioImageIO-Packager]
@@ -253,13 +236,30 @@ collection:
     tissue, confocal-microscopy, pytorch, fixed]
   type: model
   versions: ['6383430']
+- authors:
+  - {name: Constantin Pape}
+  covers: ['https://zenodo.org/api/files/ac8ecde9-bafd-4c2c-9ede-0f4a47077d31/cover.png']
+  description: Mitochondria segmentation for electron microscopy.
+  download_count: 9260
+  id: 10.5281/zenodo.5874841
+  license: CC-BY-4.0
+  links: [deepimagej/deepimagej, ilastik/ilastik, ilastik/mitoem_segmentation_challenge,
+    imjoy/BioImageIO-Packager]
+  name: MitochondriaEMSegmentationBoundaryModel
+  nickname: kind-seashell
+  nickname_icon: "\U0001F41A"
+  owners: [77626]
+  rdf_source: https://FynnBe.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.5874841/6630266/rdf.yaml
+  tags: [3d, electron-microscopy, mitochondria, instance-segmentation, unet]
+  type: model
+  versions: ['6630266', '5874842']
 - authors:
   - {name: Hao Xu}
   - {name: Wei Ouyang}
   covers: ['https://zenodo.org/api/files/858dbb84-174e-48cb-b2ef-9f1db2d0b275/hpaseg-cover.png']
   description: Cell segmentation model for segmenting images from the Human Protein
     Atlas
-  download_count: 6571
+  download_count: 6597
   id: 10.5281/zenodo.6200635
   license: CC-BY-4.0
   links: [imjoy/BioImageIO-Packager, hpa/hpa-cell-image-segmentation-dataset]
@@ -553,7 +553,7 @@ collection:
   covers: ['https://zenodo.org/api/files/0c6f4346-c936-420b-89be-322f6df574ae/hpaseg-cover.png']
   description: Nuclei segmentation model for segmenting images from the Human Protein
     Atlas
-  download_count: 3076
+  download_count: 3091
   id: 10.5281/zenodo.6200999
   license: CC-BY-4.0
   links: [deepimagej/deepimagej]
@@ -572,7 +572,7 @@ collection:
   covers: ['https://zenodo.org/api/files/5a9cfb56-3a5d-4796-986d-8f46b7987b92/cover.png']
   description: 2D UNet trained using ZeroCostDL4Mic notebooks on data from ISBI Challenge
     for neuron segmentation in Transmission Electron Microscopy images.
-  download_count: 3061
+  download_count: 3076
   id: 10.5281/zenodo.5817052
   license: MIT
   links: [imjoy/BioImageIO-Packager, zero/notebook_u-net_2d_zerocostdl4mic_deepimagej,