From 126dc266258c7b2c2b4cfe10786e31e36fabf941 Mon Sep 17 00:00:00 2001 From: FynnBe Date: Tue, 21 Nov 2023 03:26:06 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20bioimage?= =?UTF-8?q?-io/collection-bioimage-io@095fca12d35ae676ba98f1cd90da8fee8864?= =?UTF-8?q?a73d=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- collection.json | 92 ++++++++++++++++++++++++------------------------- rdf.json | 92 ++++++++++++++++++++++++------------------------- rdf.yaml | 92 ++++++++++++++++++++++++------------------------- 3 files changed, 138 insertions(+), 138 deletions(-) diff --git a/collection.json b/collection.json index a7c43126d..65466a415 100644 --- a/collection.json +++ b/collection.json @@ -23,7 +23,7 @@ ], "created": "2022-06-15 22:06:22.658325", "description": "Nucleus segmentation for fluorescence microscopy", - "download_count": 47983, + "download_count": 48175, "id": "10.5281/zenodo.5764892", "license": "CC-BY-4.0", "links": [ @@ -66,7 +66,7 @@ ], "created": "2022-01-18 22:01:09.315638", "description": "Neuron segmentation in EM, trained on the CREMI challenge data.", - "download_count": 34535, + "download_count": 34644, "id": "10.5281/zenodo.5874741", "license": "CC-BY-4.0", "links": [ @@ -112,7 +112,7 @@ ], "created": "2022-06-15 22:09:35.368273", "description": "Cell segmentation for phase-contrast microscopy.", - "download_count": 33774, + "download_count": 33828, "id": "10.5281/zenodo.5869899", "license": "CC-BY-4.0", "links": [ @@ -157,7 +157,7 @@ ], "created": "2022-06-10 06:22:28.465944", "description": "Mitochondria segmentation for electron microscopy.", - "download_count": 31207, + "download_count": 31259, "id": "10.5281/zenodo.5874841", "license": "CC-BY-4.0", "links": [ @@ -197,7 +197,7 @@ ], "created": "2022-02-09 21:14:46.430029", "description": "{organelle} segmentation in EM of platynereis.", - "download_count": 31204, + "download_count": 31244, "id": "10.5281/zenodo.6028097", "license": "CC-BY-4.0", "links": [ @@ -246,7 +246,7 @@ ], "created": "2022-03-08 18:36:28.378522", "description": "StarDist - Object Detection with Star-convex Shapes", - "download_count": 30917, + "download_count": 31027, "id": "10.5281/zenodo.6338614", "license": "BSD-3-Clause", "links": [ @@ -293,7 +293,7 @@ ], "created": "2022-06-15 22:12:29.012734", "description": "Cell segmentation in EM of platynereis.", - "download_count": 29177, + "download_count": 29238, "id": "10.5281/zenodo.6028280", "license": "CC-BY-4.0", "links": [ @@ -339,7 +339,7 @@ ], "created": "2023-07-26 10:47:44.642355", "description": "DeepImageJ compatible U-Net trained to segment phase contrast microscopy images of pancreatic stem cells on a 2D polystyrene substrate.", - "download_count": 28453, + "download_count": 28558, "id": "10.5281/zenodo.5914248", "license": "BSD-2-Clause", "links": [ @@ -395,7 +395,7 @@ ], "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.", - "download_count": 28148, + "download_count": 28223, "id": "10.5281/zenodo.5749843", "license": "MIT", "links": [ @@ -446,7 +446,7 @@ ], "created": "2023-03-06 19:01:04.321374", "description": "Cell segmentation model for segmenting images from the Human Protein Atlas", - "download_count": 27822, + "download_count": 27897, "id": "10.5281/zenodo.6200635", "license": "CC-BY-4.0", "links": [ @@ -493,7 +493,7 @@ ], "created": "2022-03-11 22:32:05.554959", "description": "StarDist - Object Detection with Star-convex Shapes", - "download_count": 27187, + "download_count": 27280, "id": "10.5281/zenodo.6348084", "license": "BSD-3-Clause", "links": [ @@ -547,7 +547,7 @@ ], "created": "2023-03-24 17:08:34.402776", "description": "3D Unet trained on confocal images of Arabidopsis thaliana apical stem cell: https://www.repository.cam.ac.uk/handle/1810/262530. 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(0.25x0.1625x0.1625) microns ZYX", - "download_count": 17229, + "download_count": 17266, "id": "10.5281/zenodo.6334777", "license": "MIT", "links": [ @@ -1265,7 +1265,7 @@ ], "created": "2022-05-11 12:52:23.766143", "description": "The winning model of HPA image classification 2021 by Bestfitting", - "download_count": 17006, + "download_count": 17064, "id": "10.5281/zenodo.5910854", "license": "MIT", "links": [ @@ -1304,7 +1304,7 @@ ], "created": "2022-02-01 22:38:38.088910", "description": "The winning model of HPA image classification 2019 by Bestfitting", - "download_count": 15487, + "download_count": 15512, "id": "10.5281/zenodo.5910163", "license": "MIT", "links": [ @@ -1342,7 +1342,7 @@ ], "created": "2022-07-08 14:35:48.861260", "description": "Prediction enhancer for segmenting mitochondria in EM images.", - "download_count": 15481, + "download_count": 15510, "id": "10.5281/zenodo.6811491", "license": "CC-BY-4.0", "links": [ @@ -1387,7 +1387,7 @@ ], "created": "2023-03-29 18:14:39.826271", "description": "This trained 2D U-Net model segments the contour, foreground and background of Bacillus Subtilis bacteria imaged with Widefield microscopy images. To obtain a unique label for each individual bacteria detected in the image one could run further watershed segmentation using the label 1 as the seed.", - "download_count": 13349, + "download_count": 13417, "id": "10.5281/zenodo.7261974", "license": "MIT", "links": [ @@ -1465,7 +1465,7 @@ ], "created": "2022-05-18 09:42:30.953891", "description": "DeepImageJ compatible fully residual U-Net trained to segment small extracellular vesicles in 2D TEM images", - "download_count": 11331, + "download_count": 11349, "download_url": "https://zenodo.org/api/records/6559475/files/deepimagej_fru-net_sev_segmentation.zip/content", "id": "10.5281/zenodo.6559474", "license": "BSD-3-Clause", @@ -1513,7 +1513,7 @@ ], "created": "2022-07-07 21:30:58.116303", "description": "Prediction enhancer for segmenting cell boundaries in EM images.", - "download_count": 9954, + "download_count": 9995, "id": "10.5281/zenodo.6808325", "license": "CC-BY-4.0", "links": [ @@ -1559,7 +1559,7 @@ ], "created": "2023-07-07 10:12:51.478763", "description": "Cellular membrane prediction model for volume SEM datasets", - "download_count": 8751, + "download_count": 8786, "id": "10.5281/zenodo.7274275", "license": "CC-BY-4.0", "links": [ @@ -1623,7 +1623,7 @@ ], "created": "2022-11-12 12:53:32.701172", "description": "EmbryoNet Model by embryoNet Team", - "download_count": 6834, + "download_count": 6899, "id": "10.5281/zenodo.7315440", "license": "GPL-3.0", "links": [ @@ -1670,7 +1670,7 @@ ], "created": "2022-12-06 13:55:39.060882", "description": "For segmenting 2D projections of drosophila epithelia", - "download_count": 6385, + "download_count": 6410, "id": "10.5281/zenodo.7380171", "license": "CC-BY-4.0", "name": "Drosophila epithelia cell boundary segmentation of 2D projections", @@ -1710,7 +1710,7 @@ ], "created": "2023-03-29 11:10:26.329999", "description": "Unet trained on confocal images of Arabidopsis Ovules nuclei", - "download_count": 6263, + "download_count": 6291, "id": "10.5281/zenodo.7772662", "license": "MIT", "links": [ @@ -1772,7 +1772,7 @@ ], "created": "2022-05-18 10:12:14.635800", "description": "DeepImageJ compatible fully residual U-Net trained to segment small extracellular vesicles in 2D TEM images", - "download_count": 5982, + "download_count": 5984, "download_url": "https://cbia.fi.muni.cz/files/segmentation/fru-net/FRU_processing.zip", "id": "10.5281/zenodo.6559929", "license": "MIT", @@ -1812,7 +1812,7 @@ ], "created": "2023-02-15 09:34:43.433531", "description": "HyLFM-Net trained on static images of arrested medaka hatchling hearts. The network reconstructs a volumentric image from a given light-field.", - "download_count": 4861, + "download_count": 4905, "id": "10.5281/zenodo.7614645", "license": "MIT", "links": [ @@ -1861,7 +1861,7 @@ ], "created": "2023-03-30 16:57:43.433376", "description": "Wasserstein GAN (WGAN) trained for super-resolution of confocal scanning microscopy images of mitochondria in U2OS cells. Mitochondria were labelled with MitoTracker and the model was trained to upsample the images by a factor of 4.", - "download_count": 3490, + "download_count": 3529, "id": "10.5281/zenodo.7786492", "license": "MIT", "links": [ @@ -1904,7 +1904,7 @@ ], "created": "2023-02-06 13:30:05.714615", "description": "Light-sheet and light-field images of beating and arrested hatchling (8 dpf) medaka hearts used in \"Deep learning-enhanced light-field imaging with continuous validation\" to train and evaluate a HyLFM-Net.", - "download_count": 1993, + "download_count": 1997, "id": "10.5281/zenodo.7612115", "license": "MIT", "name": "Hatchling Medaka Heart (HyLFM)", @@ -1940,7 +1940,7 @@ ], "created": "2023-06-23 10:23:37.255827", "description": "Label-free prediction of fluorescence images from brightield images", - "download_count": 1835, + "download_count": 1839, "id": "10.5281/zenodo.8064806", "license": "Apache-2.0", "links": [ @@ -1979,7 +1979,7 @@ ], "created": "2023-07-21 09:09:49.349470", "description": "Prediction enhancer for segmenting cell boundaries in EM images.", - "download_count": 1325, + "download_count": 1331, "id": "10.5281/zenodo.8142283", "license": "MIT", "links": [ @@ -2022,7 +2022,7 @@ ], "created": "2023-10-11 17:13:48.737609", "description": "This widely applicable model is trained for 3D nuclei instance segmentation and with 3D nuclei images of Arabidopsis ovules with TO-PRO-3 stain. TO-PRO-3 nuclei stain detects double-stranded nucleic acids and hence can be a useful tool for nuclear DNA quantification and 3D volumetric nuclei extraction. This model is trained with dataset 1136, 1137, 1139, 1170 and validated with 1135.", - "download_count": 1013, + "download_count": 1033, "id": "10.5281/zenodo.8421755", "license": "CC-BY-4.0", "links": [ @@ -2080,7 +2080,7 @@ ], "created": "2023-10-09 06:57:28.189519", "description": "Pre-training a Foundation Model for Universal Fluorescence Microscopy Image Restoration", - "download_count": 775, + "download_count": 796, "id": "10.5281/zenodo.8419845", "license": "CC-BY-4.0", "name": "UniFMIRSuperResolutionOnMicrotubules", @@ -2118,7 +2118,7 @@ ], "created": "2023-10-11 00:39:40.958129", "description": "This widely applicable model is trained for 3D nuclei instance segmentation and with 3D nuclei images of Arabidopsis ovules with TO-PRO-3 stain. TO-PRO-3 nuclei stain detects double-stranded nucleic acids and hence can be a useful tool for nuclear DNA quantification and 3D volumetric nuclei extraction. This model is trained with dataset 1136, 1137, 1139, 1170 and validated with 1135. Patch size for this model during inference can be flexible.", - "download_count": 619, + "download_count": 629, "id": "10.5281/zenodo.8401064", "license": "CC-BY-4.0", "links": [ @@ -2177,7 +2177,7 @@ ], "created": "2023-10-09 07:05:52.763368", "description": "Pre-training a Foundation Model for Universal Fluorescence Microscopy Image Restoration", - "download_count": 476, + "download_count": 504, "id": "10.5281/zenodo.8420099", "license": "CC-BY-4.0", "links": [ diff --git a/rdf.yaml b/rdf.yaml index 866f46360..0ce672017 100644 --- a/rdf.yaml +++ b/rdf.yaml @@ -8,7 +8,7 @@ collection: covers: ['https://bioimage-io.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.5764892/6322939/cover.png'] created: '2022-06-15 22:06:22.658325' description: Nucleus segmentation for fluorescence microscopy - download_count: 47983 + download_count: 48175 id: 10.5281/zenodo.5764892 license: CC-BY-4.0 links: [ilastik/stardist_dsb_training_data, ilastik/ilastik, deepimagej/deepimagej, @@ -27,7 +27,7 @@ collection: covers: ['https://bioimage-io.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.5874741/5874742/cover.png'] created: '2022-01-18 22:01:09.315638' description: Neuron segmentation in EM, trained on the CREMI challenge data. - download_count: 34535 + download_count: 34644 id: 10.5281/zenodo.5874741 license: CC-BY-4.0 links: [deepimagej/deepimagej, ilastik/ilastik, imjoy/BioImageIO-Packager, ilastik/torch-em-3d-unet-notebook] @@ -46,7 +46,7 @@ collection: covers: ['https://bioimage-io.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.5869899/5869900/cover.png'] created: '2022-06-15 22:09:35.368273' description: Cell segmentation for phase-contrast microscopy. - download_count: 33774 + download_count: 33828 id: 10.5281/zenodo.5869899 license: CC-BY-4.0 links: [ilastik/livecell_dataset, ilastik/ilastik, deepimagej/deepimagej, imjoy/BioImageIO-Packager] @@ -65,7 +65,7 @@ collection: covers: ['https://bioimage-io.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.5874841/5874842/cover.png'] created: '2022-06-10 06:22:28.465944' description: Mitochondria segmentation for electron microscopy. - download_count: 31207 + download_count: 31259 id: 10.5281/zenodo.5874841 license: CC-BY-4.0 links: [deepimagej/deepimagej, ilastik/ilastik, ilastik/mitoem_segmentation_challenge, @@ -83,7 +83,7 @@ collection: covers: ['https://bioimage-io.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.6028097/6028098/cover.png'] created: '2022-02-09 21:14:46.430029' description: '{organelle} segmentation in EM of platynereis.' - download_count: 31204 + download_count: 31244 id: 10.5281/zenodo.6028097 license: CC-BY-4.0 links: [deepimagej/deepimagej, ilastik/ilastik, imjoy/BioImageIO-Packager, ilastik/torch-em-3d-unet-notebook] @@ -103,7 +103,7 @@ collection: 'https://bioimage-io.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.6338614/6338615/example_histo.jpg'] created: '2022-03-08 18:36:28.378522' description: StarDist - Object Detection with Star-convex Shapes - download_count: 30917 + download_count: 31027 id: 10.5281/zenodo.6338614 license: BSD-3-Clause links: [deepimagej/deepimagej, imjoy/BioImageIO-Packager, ilastik/tnbc, bioimageio/stardist, @@ -123,7 +123,7 @@ collection: covers: ['https://bioimage-io.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.6028280/6028281/cover.png'] created: '2022-06-15 22:12:29.012734' description: Cell segmentation in EM of platynereis. - download_count: 29177 + download_count: 29238 id: 10.5281/zenodo.6028280 license: CC-BY-4.0 links: [deepimagej/deepimagej, ilastik/platynereis_em_training_data, ilastik/ilastik, @@ -144,7 +144,7 @@ collection: created: '2023-07-26 10:47:44.642355' description: DeepImageJ compatible U-Net trained to segment phase contrast microscopy images of pancreatic stem cells on a 2D polystyrene substrate. - download_count: 28453 + download_count: 28558 id: 10.5281/zenodo.5914248 license: BSD-2-Clause links: [imjoy/BioImageIO-Packager, deepimagej/deepimagej, ilastik/ilastik, deepimagej/unet-pancreaticcellsegmentation, @@ -167,7 +167,7 @@ collection: 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. - download_count: 28148 + download_count: 28223 id: 10.5281/zenodo.5749843 license: MIT links: [imjoy/BioImageIO-Packager, ilastik/ilastik, deepimagej/deepimagej, zero/notebook_u-net_3d_zerocostdl4mic] @@ -188,7 +188,7 @@ collection: created: '2023-03-06 19:01:04.321374' description: Cell segmentation model for segmenting images from the Human Protein Atlas - download_count: 27822 + download_count: 27897 id: 10.5281/zenodo.6200635 license: CC-BY-4.0 links: [deepimagej/deepimagej, hpa/hpa-cell-image-segmentation-dataset, imjoy/BioImageIO-Packager, @@ -208,7 +208,7 @@ collection: 'https://bioimage-io.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.6348084/6348085/example_fluo.jpg'] created: '2022-03-11 22:32:05.554959' description: StarDist - Object Detection with Star-convex Shapes - download_count: 27187 + download_count: 27280 id: 10.5281/zenodo.6348084 license: BSD-3-Clause links: [deepimagej/deepimagej, imjoy/BioImageIO-Packager, bioimageio/stardist, bioimageio/qupath, @@ -232,7 +232,7 @@ collection: description: '3D Unet trained on confocal images of Arabidopsis thaliana apical stem cell: https://www.repository.cam.ac.uk/handle/1810/262530. Voxel size: [0.25, 0.25, 0.25]' - download_count: 27054 + download_count: 27108 id: 10.5281/zenodo.6346511 license: MIT links: [deepimagej/deepimagej, imjoy/BioImageIO-Packager, ilastik/ilastik] @@ -250,7 +250,7 @@ collection: covers: ['https://bioimage-io.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.6348728/6348729/cover.png'] created: '2022-03-12 09:56:33.055323' description: Perform leaf segmentation in light microscopy images of Arabidopsis - download_count: 26990 + download_count: 27100 id: 10.5281/zenodo.6348728 license: MIT links: [deepimagej/deepimagej, imjoy/BioImageIO-Packager, ilastik/ilastik, zero/notebook_u-net_3d_zerocostdl4mic] @@ -268,7 +268,7 @@ collection: covers: ['https://bioimage-io.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.6406803/6406804/cover.png'] created: '2022-04-01 16:06:28.519947' description: Segmentation of mitochondria in EM images. - download_count: 25507 + download_count: 25554 id: 10.5281/zenodo.6406803 license: CC-BY-4.0 links: [deepimagej/deepimagej, ilastik/ilastik, imjoy/BioImageIO-Packager, ilastik/torch-em-2d-unet-notebook] @@ -286,7 +286,7 @@ collection: covers: ['https://bioimage-io.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.5847355/6322908/cover.png'] created: '2022-06-15 22:08:13.874556' description: Cell segmentation for immunofluorescence microscopy. - download_count: 25430 + download_count: 25477 id: 10.5281/zenodo.5847355 license: CC-BY-4.0 links: [ilastik/covid_if_training_data, ilastik/ilastik, deepimagej/deepimagej, @@ -309,7 +309,7 @@ collection: created: '2022-01-27 14:00:17.489637' description: 2D UNet trained using ZeroCostDL4Mic notebooks on data from ISBI Challenge for neuron segmentation in Transmission Electron Microscopy images. - download_count: 24015 + download_count: 24079 id: 10.5281/zenodo.5817052 license: MIT links: [imjoy/BioImageIO-Packager, zero/notebook_u-net_2d_zerocostdl4mic_deepimagej, @@ -330,7 +330,7 @@ collection: created: '2023-03-02 05:53:45.695883' description: Nuclei segmentation model for segmenting images from the Human Protein Atlas - download_count: 23819 + download_count: 23886 id: 10.5281/zenodo.6200999 license: CC-BY-4.0 links: [deepimagej/deepimagej, ilastik/ilastik] @@ -350,7 +350,7 @@ collection: created: '2023-03-27 12:11:52.357154' description: 'A 3D U-Net trained to predict the cell boundaries in live light sheet images of developing mouse embryo. Voxel size: 0.2×0.2×1.0 µm^3' - download_count: 23459 + download_count: 23474 id: 10.5281/zenodo.6384845 license: MIT links: [deepimagej/deepimagej, imjoy/BioImageIO-Packager, ilastik/ilastik] @@ -368,7 +368,7 @@ collection: covers: ['https://bioimage-io.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.6406756/6406757/cover.png'] created: '2022-07-08 17:02:28.049385' description: Prediction enhancer for segmenting mitochondria in EM images. - download_count: 22292 + download_count: 22356 id: 10.5281/zenodo.6406756 license: CC-BY-4.0 links: [ilastik/torch-em-2d-unet-notebook, ilastik/ilastik, deepimagej/deepimagej, @@ -392,7 +392,7 @@ collection: created: '2023-03-27 12:14:49.467153' 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: 21602 + download_count: 21673 id: 10.5281/zenodo.6383429 license: MIT links: [deepimagej/deepimagej, imjoy/BioImageIO-Packager, ilastik/ilastik] @@ -411,7 +411,7 @@ collection: 'https://bioimage-io.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.6334383/6334384/pred.png'] created: '2023-04-06 10:47:26.453147' description: 2D Unet trained on confocal images of Arabidopsis Ovules - download_count: 21147 + download_count: 21155 id: 10.5281/zenodo.6334383 license: MIT links: [imjoy/BioImageIO-Packager, ilastik/ilastik] @@ -429,7 +429,7 @@ collection: covers: ['https://bioimage-io.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.6079314/6079315/cover.png'] created: '2023-03-03 13:09:05.981223' description: affinity-model - download_count: 19662 + download_count: 19670 id: 10.5281/zenodo.6079314 license: CC-BY-4.0 links: [imjoy/BioImageIO-Packager, ilastik/torch-em-2d-unet-notebook, ilastik/ilastik, @@ -450,7 +450,7 @@ collection: created: '2023-04-06 10:26:25.873589' description: 2D Unet trained on z-slices of confocal images of Arabidopsis thaliana apical stem cells - download_count: 18953 + download_count: 18970 id: 10.5281/zenodo.6334881 license: MIT links: [imjoy/BioImageIO-Packager, ilastik/ilastik] @@ -472,7 +472,7 @@ collection: created: '2023-04-06 12:43:33.436336' description: 'A 3d U-Net trained to predict the cell boundaries in confocal stacks of Arabidopsis ovules. Voxel size: (0.235, 0.150, 0.150) microns ZYX' - download_count: 17581 + download_count: 17587 id: 10.5281/zenodo.6334583 license: MIT links: [imjoy/BioImageIO-Packager, ilastik/ilastik] @@ -491,7 +491,7 @@ collection: 'https://bioimage-io.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.6865412/6919253/lable.png'] created: '2022-07-28 07:37:36.393648' description: DeepImageJ compatible FRUNet trained to subtly segment cells and gland. - download_count: 17496 + download_count: 17514 id: 10.5281/zenodo.6865412 license: CC-BY-4.0 name: Cells and gland Segmentation (FRUNet) @@ -510,7 +510,7 @@ collection: created: '2023-03-23 21:42:30.250688' description: A 3D U-Net trained to predict the cell boundaries in lightsheet stacks of Arabidopsis Lateral Root Primordia. (0.25x0.1625x0.1625) microns ZYX - download_count: 17229 + download_count: 17266 id: 10.5281/zenodo.6334777 license: MIT links: [deepimagej/deepimagej, imjoy/BioImageIO-Packager, ilastik/ilastik] @@ -529,7 +529,7 @@ collection: covers: ['https://bioimage-io.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.5910854/5911832/diagram-of-InceptionV3.png'] created: '2022-05-11 12:52:23.766143' description: The winning model of HPA image classification 2021 by Bestfitting - download_count: 17006 + download_count: 17064 id: 10.5281/zenodo.5910854 license: MIT links: [imjoy/BioImageIO-Packager, hpa/hpa-kaggle-2021-dataset] @@ -546,7 +546,7 @@ collection: covers: ['https://bioimage-io.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.5910163/5942853/bestfitting-densenet-diagram.png'] created: '2022-02-01 22:38:38.088910' description: The winning model of HPA image classification 2019 by Bestfitting - download_count: 15487 + download_count: 15512 id: 10.5281/zenodo.5910163 license: MIT links: [imjoy/BioImageIO-Packager] @@ -563,7 +563,7 @@ collection: covers: ['https://bioimage-io.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.6811491/6811492/cover.png'] created: '2022-07-08 14:35:48.861260' description: Prediction enhancer for segmenting mitochondria in EM images. - download_count: 15481 + download_count: 15510 id: 10.5281/zenodo.6811491 license: CC-BY-4.0 links: [deepimagej/deepimagej, ilastik/torch-em-3d-unet-notebook, ilastik/ilastik, @@ -587,7 +587,7 @@ collection: of Bacillus Subtilis bacteria imaged with Widefield microscopy images. To obtain a unique label for each individual bacteria detected in the image one could run further watershed segmentation using the label 1 as the seed. - download_count: 13349 + download_count: 13417 id: 10.5281/zenodo.7261974 license: MIT links: [deepimagej/deepimagej, imjoy/BioImageIO-Packager, zero/dataset_u-net_2d_multilabel_deepbacs, @@ -615,7 +615,7 @@ collection: created: '2022-05-18 09:42:30.953891' description: DeepImageJ compatible fully residual U-Net trained to segment small extracellular vesicles in 2D TEM images - download_count: 11331 + download_count: 11349 download_url: https://zenodo.org/api/records/6559475/files/deepimagej_fru-net_sev_segmentation.zip/content id: 10.5281/zenodo.6559474 license: BSD-3-Clause @@ -635,7 +635,7 @@ collection: covers: ['https://bioimage-io.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.6808325/6808413/cover.png'] created: '2022-07-07 21:30:58.116303' description: Prediction enhancer for segmenting cell boundaries in EM images. - download_count: 9954 + download_count: 9995 id: 10.5281/zenodo.6808325 license: CC-BY-4.0 links: [ilastik/ilastik, deepimagej/deepimagej, ilastik/torch-em-3d-unet-notebook, @@ -654,7 +654,7 @@ collection: covers: ['https://bioimage-io.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.7274275/7274276/coverimage.jpg'] created: '2023-07-07 10:12:51.478763' description: Cellular membrane prediction model for volume SEM datasets - download_count: 8751 + download_count: 8786 id: 10.5281/zenodo.7274275 license: CC-BY-4.0 links: [deepimagej/deepimagej] @@ -677,7 +677,7 @@ collection: covers: ['https://bioimage-io.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.7315440/7315441/phenotypes_features.png'] created: '2022-11-12 12:53:32.701172' description: EmbryoNet Model by embryoNet Team - download_count: 6834 + download_count: 6899 id: 10.5281/zenodo.7315440 license: GPL-3.0 links: [Embryonet.de, imjoy/BioImageIO-Packager] @@ -697,7 +697,7 @@ collection: covers: ['https://bioimage-io.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.7380171/7405349/cover.png'] created: '2022-12-06 13:55:39.060882' description: For segmenting 2D projections of drosophila epithelia - download_count: 6385 + download_count: 6410 id: 10.5281/zenodo.7380171 license: CC-BY-4.0 name: Drosophila epithelia cell boundary segmentation of 2D projections @@ -716,7 +716,7 @@ collection: 'https://bioimage-io.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.7772662/7781091/pmaps.png'] created: '2023-03-29 11:10:26.329999' description: Unet trained on confocal images of Arabidopsis Ovules nuclei - download_count: 6263 + download_count: 6291 id: 10.5281/zenodo.7772662 license: MIT links: [imjoy/BioImageIO-Packager] @@ -740,7 +740,7 @@ collection: created: '2022-05-18 10:12:14.635800' description: DeepImageJ compatible fully residual U-Net trained to segment small extracellular vesicles in 2D TEM images - download_count: 5982 + download_count: 5984 download_url: https://cbia.fi.muni.cz/files/segmentation/fru-net/FRU_processing.zip id: 10.5281/zenodo.6559929 license: MIT @@ -759,7 +759,7 @@ collection: created: '2023-02-15 09:34:43.433531' description: HyLFM-Net trained on static images of arrested medaka hatchling hearts. The network reconstructs a volumentric image from a given light-field. - download_count: 4861 + download_count: 4905 id: 10.5281/zenodo.7614645 license: MIT links: [imjoy/BioImageIO-Packager] @@ -782,7 +782,7 @@ collection: description: Wasserstein GAN (WGAN) trained for super-resolution of confocal scanning microscopy images of mitochondria in U2OS cells. Mitochondria were labelled with MitoTracker and the model was trained to upsample the images by a factor of 4. - download_count: 3490 + download_count: 3529 id: 10.5281/zenodo.7786492 license: MIT links: [deepimagej/deepimagej, imjoy/BioImageIO-Packager] @@ -802,7 +802,7 @@ collection: description: Light-sheet and light-field images of beating and arrested hatchling (8 dpf) medaka hearts used in "Deep learning-enhanced light-field imaging with continuous validation" to train and evaluate a HyLFM-Net. - download_count: 1993 + download_count: 1997 id: 10.5281/zenodo.7612115 license: MIT name: Hatchling Medaka Heart (HyLFM) @@ -819,7 +819,7 @@ collection: covers: ['https://bioimage-io.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.8064806/8073617/cover.png'] created: '2023-06-23 10:23:37.255827' description: Label-free prediction of fluorescence images from brightield images - download_count: 1835 + download_count: 1839 id: 10.5281/zenodo.8064806 license: Apache-2.0 links: [imjoy/BioImageIO-Packager] @@ -836,7 +836,7 @@ collection: covers: ['https://bioimage-io.github.io/collection-bioimage-io/rdfs/10.5281/zenodo.8142283/8171247/cover.png'] created: '2023-07-21 09:09:49.349470' description: Prediction enhancer for segmenting cell boundaries in EM images. - download_count: 1325 + download_count: 1331 id: 10.5281/zenodo.8142283 license: MIT links: [imjoy/BioImageIO-Packager] @@ -860,7 +860,7 @@ collection: nuclei stain detects double-stranded nucleic acids and hence can be a useful tool for nuclear DNA quantification and 3D volumetric nuclei extraction. This model is trained with dataset 1136, 1137, 1139, 1170 and validated with 1135. - download_count: 1013 + download_count: 1033 id: 10.5281/zenodo.8421755 license: CC-BY-4.0 links: [imjoy/BioImageIO-Packager] @@ -883,7 +883,7 @@ collection: created: '2023-10-09 06:57:28.189519' description: Pre-training a Foundation Model for Universal Fluorescence Microscopy Image Restoration - download_count: 775 + download_count: 796 id: 10.5281/zenodo.8419845 license: CC-BY-4.0 name: UniFMIRSuperResolutionOnMicrotubules @@ -907,7 +907,7 @@ collection: for nuclear DNA quantification and 3D volumetric nuclei extraction. This model is trained with dataset 1136, 1137, 1139, 1170 and validated with 1135. Patch size for this model during inference can be flexible. - download_count: 619 + download_count: 629 id: 10.5281/zenodo.8401064 license: CC-BY-4.0 links: [imjoy/BioImageIO-Packager] @@ -930,7 +930,7 @@ collection: created: '2023-10-09 07:05:52.763368' description: Pre-training a Foundation Model for Universal Fluorescence Microscopy Image Restoration - download_count: 476 + download_count: 504 id: 10.5281/zenodo.8420099 license: CC-BY-4.0 links: [imjoy/BioImageIO-Packager]