diff --git a/collection.json b/collection.json index 3ac3878090..c6f0c8e183 100644 --- 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, - 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"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 index 898e1bedd4..11ee025500 100644 --- 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,