From d2c39917866f9b4635b5af9768fb192b6e139cc4 Mon Sep 17 00:00:00 2001 From: FynnBe Date: Mon, 5 Feb 2024 03:24:08 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20bioimage?= =?UTF-8?q?-io/collection-bioimage-io@a66b64ddba58073e13aa83e16e342b7fd06e?= =?UTF-8?q?0b3d=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 0113ca69e..973713be1 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": 57020, + "download_count": 57127, "id": "10.5281/zenodo.5764892", "license": "CC-BY-4.0", "links": [ @@ -72,7 +72,7 @@ ], "created": "2022-03-08 18:36:28.378522", "description": "StarDist - Object Detection with Star-convex Shapes", - "download_count": 41758, + "download_count": 41823, "id": "10.5281/zenodo.6338614", "license": "BSD-3-Clause", "links": [ @@ -118,7 +118,7 @@ ], "created": "2022-01-18 22:01:09.315638", "description": "Neuron segmentation in EM, trained on the CREMI challenge data.", - "download_count": 39707, + "download_count": 39772, "id": "10.5281/zenodo.5874741", "license": "CC-BY-4.0", "links": [ @@ -164,7 +164,7 @@ ], "created": "2022-06-15 22:09:35.368273", "description": "Cell segmentation for phase-contrast microscopy.", - "download_count": 39385, + "download_count": 39388, "id": "10.5281/zenodo.5869899", "license": "CC-BY-4.0", "links": [ @@ -209,7 +209,7 @@ ], "created": "2022-06-10 06:22:28.465944", "description": "Mitochondria segmentation for electron microscopy.", - "download_count": 35735, + "download_count": 35801, "id": "10.5281/zenodo.5874841", "license": "CC-BY-4.0", "links": [ @@ -249,7 +249,7 @@ ], "created": "2022-02-09 21:14:46.430029", "description": "{organelle} segmentation in EM of platynereis.", - "download_count": 35451, + "download_count": 35516, "id": "10.5281/zenodo.6028097", "license": "CC-BY-4.0", "links": [ @@ -298,7 +298,7 @@ ], "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": 35216, + "download_count": 35295, "id": "10.5281/zenodo.5914248", "license": "BSD-2-Clause", "links": [ @@ -354,7 +354,7 @@ ], "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": 34380, + "download_count": 34456, "id": "10.5281/zenodo.5749843", "license": "MIT", "links": [ @@ -402,7 +402,7 @@ ], "created": "2022-06-15 22:12:29.012734", "description": "Cell segmentation in EM of platynereis.", - "download_count": 33334, + "download_count": 33392, "id": "10.5281/zenodo.6028280", "license": "CC-BY-4.0", "links": [ @@ -448,7 +448,7 @@ ], "created": "2022-03-11 22:32:05.554959", "description": "StarDist - Object Detection with Star-convex Shapes", - "download_count": 33124, + "download_count": 33189, "id": "10.5281/zenodo.6348084", "license": "BSD-3-Clause", "links": [ @@ -500,7 +500,7 @@ ], "created": "2023-03-06 19:01:04.321374", "description": "Cell segmentation model for segmenting images from the Human Protein Atlas", - "download_count": 32248, + "download_count": 32300, "id": "10.5281/zenodo.6200635", "license": "CC-BY-4.0", "links": [ @@ -541,7 +541,7 @@ ], "created": "2022-03-12 09:56:33.055323", "description": "Perform leaf segmentation in light microscopy images of Arabidopsis", - "download_count": 31768, + "download_count": 31769, "id": "10.5281/zenodo.6348728", "license": "MIT", "links": [ @@ -586,7 +586,7 @@ ], "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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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": 24837, + "download_count": 24950, "id": "10.5281/zenodo.7261974", "license": "MIT", "links": [ @@ -1025,7 +1025,7 @@ ], "created": "2023-03-03 13:09:05.981223", "description": "affinity-model", - "download_count": 24262, + "download_count": 24362, "id": "10.5281/zenodo.6079314", "license": "CC-BY-4.0", "links": [ @@ -1073,7 +1073,7 @@ ], "created": "2023-04-06 10:47:26.453147", "description": "2D Unet trained on confocal images of Arabidopsis Ovules", - "download_count": 23957, + "download_count": 24021, "id": "10.5281/zenodo.6334383", "license": "MIT", "links": [ @@ -1124,7 +1124,7 @@ ], "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": 21891, + "download_count": 21955, "id": "10.5281/zenodo.6334881", "license": "MIT", "links": [ @@ -1172,7 +1172,7 @@ ], "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. 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Voxel size: (0.235, 0.150, 0.150) microns ZYX", - "download_count": 20334, + "download_count": 20390, "id": "10.5281/zenodo.6334583", "license": "MIT", "links": [ @@ -1319,7 +1319,7 @@ ], "created": "2022-07-08 14:35:48.861260", "description": "Prediction enhancer for segmenting mitochondria in EM images.", - "download_count": 19461, + "download_count": 19571, "id": "10.5281/zenodo.6811491", "license": "CC-BY-4.0", "links": [ @@ -1364,7 +1364,7 @@ ], "created": "2022-07-28 07:37:36.393648", "description": "DeepImageJ compatible FRUNet trained to subtly segment cells and gland.", - "download_count": 18834, + "download_count": 18842, "id": "10.5281/zenodo.6865412", "license": "CC-BY-4.0", "name": "Cells and gland Segmentation (FRUNet)", @@ -1396,7 +1396,7 @@ ], "created": "2022-02-01 22:38:38.088910", "description": "The winning model of HPA image classification 2019 by Bestfitting", - "download_count": 18385, + "download_count": 18417, "id": "10.5281/zenodo.5910163", "license": "MIT", "links": [ @@ -1454,7 +1454,7 @@ ], "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": 17174, + "download_count": 17298, "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", @@ -1502,7 +1502,7 @@ ], "created": "2022-07-07 21:30:58.116303", "description": "Prediction enhancer for segmenting cell boundaries in EM images.", - "download_count": 14196, + "download_count": 14282, "id": "10.5281/zenodo.6808325", "license": "CC-BY-4.0", "links": [ @@ -1548,7 +1548,7 @@ ], "created": "2023-07-07 10:12:51.478763", "description": "Cellular membrane prediction model for volume SEM datasets", - "download_count": 13619, + "download_count": 13708, "id": "10.5281/zenodo.7274275", "license": "CC-BY-4.0", "links": [ @@ -1612,7 +1612,7 @@ ], "created": "2022-11-12 12:53:32.701172", "description": "EmbryoNet Model by embryoNet Team", - "download_count": 10349, + "download_count": 10387, "id": "10.5281/zenodo.7315440", "license": "GPL-3.0", "links": [ @@ -1659,7 +1659,7 @@ ], "created": "2022-12-06 13:55:39.060882", "description": "For segmenting 2D projections of drosophila epithelia", - "download_count": 9476, + "download_count": 9539, "id": "10.5281/zenodo.7380171", "license": "CC-BY-4.0", "name": "Drosophila epithelia cell boundary segmentation of 2D projections", @@ -1699,7 +1699,7 @@ ], "created": "2023-03-29 11:10:26.329999", "description": "Unet trained on confocal images of Arabidopsis Ovules nuclei", - "download_count": 9188, + "download_count": 9246, "id": "10.5281/zenodo.7772662", "license": "MIT", "links": [ @@ -1742,7 +1742,7 @@ ], "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": 8823, + "download_count": 8909, "id": "10.5281/zenodo.7614645", "license": "MIT", "links": [ @@ -1791,7 +1791,7 @@ ], "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": 6565, + "download_count": 6625, "id": "10.5281/zenodo.7786492", "license": "MIT", "links": [ @@ -1853,7 +1853,7 @@ ], "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": 6235, + "download_count": 6237, "download_url": "https://cbia.fi.muni.cz/files/segmentation/fru-net/FRU_processing.zip", "id": "10.5281/zenodo.6559929", "license": "MIT", @@ -1897,7 +1897,7 @@ ], "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": 4128, + "download_count": 4180, "id": "10.5281/zenodo.8421755", "license": "CC-BY-4.0", "links": [ @@ -1944,7 +1944,7 @@ ], "created": "2023-06-23 10:23:37.255827", "description": "Label-free prediction of fluorescence images from brightield images", - "download_count": 4010, + "download_count": 4060, "id": "10.5281/zenodo.8064806", "license": "Apache-2.0", "links": [ @@ -1995,7 +1995,7 @@ ], "created": "2023-10-09 06:57:28.189519", "description": "Pre-training a Foundation Model for Universal Fluorescence Microscopy Image Restoration", - "download_count": 3000, + "download_count": 3040, "id": "10.5281/zenodo.8419845", "license": "CC-BY-4.0", "name": "UniFMIRSuperResolutionOnMicrotubules", @@ -2041,7 +2041,7 @@ ], "created": "2023-10-09 07:05:52.763368", "description": "Pre-training a Foundation Model for Universal Fluorescence Microscopy Image Restoration", - "download_count": 2354, + "download_count": 2391, "id": "10.5281/zenodo.8420099", "license": "CC-BY-4.0", "links": [ @@ -2078,7 +2078,7 @@ ], "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": 2119, + "download_count": 2120, "id": "10.5281/zenodo.7612115", "license": "MIT", "name": "Hatchling Medaka Heart (HyLFM)", @@ -2113,7 +2113,7 @@ ], "created": "2023-07-21 09:09:49.349470", "description": "Prediction enhancer for segmenting cell boundaries in EM images.", - "download_count": 1753, + "download_count": 1755, "id": "10.5281/zenodo.8142283", "license": "MIT", "links": [ @@ -2156,7 +2156,7 @@ ], "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": 1377, + "download_count": 1380, "id": "10.5281/zenodo.8401064", "license": "CC-BY-4.0", "links": [ diff --git a/rdf.yaml b/rdf.yaml index 9fdfa76b8..40dec2cdf 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: 57020 + download_count: 57127 id: 10.5281/zenodo.5764892 license: CC-BY-4.0 links: [ilastik/stardist_dsb_training_data, ilastik/ilastik, deepimagej/deepimagej, @@ -29,7 +29,7 @@ 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: 41758 + download_count: 41823 id: 10.5281/zenodo.6338614 license: BSD-3-Clause links: [deepimagej/deepimagej, imjoy/BioImageIO-Packager, ilastik/tnbc, bioimageio/stardist, @@ -49,7 +49,7 @@ 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: 39707 + download_count: 39772 id: 10.5281/zenodo.5874741 license: CC-BY-4.0 links: [deepimagej/deepimagej, ilastik/ilastik, imjoy/BioImageIO-Packager, ilastik/torch-em-3d-unet-notebook] @@ -68,7 +68,7 @@ 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: 39385 + download_count: 39388 id: 10.5281/zenodo.5869899 license: CC-BY-4.0 links: [ilastik/livecell_dataset, ilastik/ilastik, deepimagej/deepimagej, imjoy/BioImageIO-Packager] @@ -87,7 +87,7 @@ 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: 35735 + download_count: 35801 id: 10.5281/zenodo.5874841 license: CC-BY-4.0 links: [deepimagej/deepimagej, ilastik/ilastik, ilastik/mitoem_segmentation_challenge, @@ -105,7 +105,7 @@ 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: 35451 + download_count: 35516 id: 10.5281/zenodo.6028097 license: CC-BY-4.0 links: [deepimagej/deepimagej, ilastik/ilastik, imjoy/BioImageIO-Packager, ilastik/torch-em-3d-unet-notebook] @@ -126,7 +126,7 @@ 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: 35216 + download_count: 35295 id: 10.5281/zenodo.5914248 license: BSD-2-Clause links: [imjoy/BioImageIO-Packager, deepimagej/deepimagej, ilastik/ilastik, deepimagej/unet-pancreaticcellsegmentation, @@ -149,7 +149,7 @@ 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: 34380 + download_count: 34456 id: 10.5281/zenodo.5749843 license: MIT links: [imjoy/BioImageIO-Packager, ilastik/ilastik, deepimagej/deepimagej, zero/notebook_u-net_3d_zerocostdl4mic] @@ -168,7 +168,7 @@ 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: 33334 + download_count: 33392 id: 10.5281/zenodo.6028280 license: CC-BY-4.0 links: [deepimagej/deepimagej, ilastik/platynereis_em_training_data, ilastik/ilastik, @@ -188,7 +188,7 @@ 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: 33124 + download_count: 33189 id: 10.5281/zenodo.6348084 license: BSD-3-Clause links: [deepimagej/deepimagej, imjoy/BioImageIO-Packager, bioimageio/stardist, bioimageio/qupath] @@ -209,7 +209,7 @@ collection: created: '2023-03-06 19:01:04.321374' description: Cell segmentation model for segmenting images from the Human Protein Atlas - download_count: 32248 + download_count: 32300 id: 10.5281/zenodo.6200635 license: CC-BY-4.0 links: [deepimagej/deepimagej, hpa/hpa-cell-image-segmentation-dataset, imjoy/BioImageIO-Packager] @@ -226,7 +226,7 @@ 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: 31768 + download_count: 31769 id: 10.5281/zenodo.6348728 license: MIT links: [deepimagej/deepimagej, imjoy/BioImageIO-Packager, ilastik/ilastik, zero/notebook_u-net_3d_zerocostdl4mic] @@ -248,7 +248,7 @@ 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: 31630 + download_count: 31682 id: 10.5281/zenodo.6346511 license: MIT links: [deepimagej/deepimagej, imjoy/BioImageIO-Packager] @@ -266,7 +266,7 @@ 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: 30583 + download_count: 30698 id: 10.5281/zenodo.6406756 license: CC-BY-4.0 links: [ilastik/torch-em-2d-unet-notebook, ilastik/ilastik, deepimagej/deepimagej, @@ -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: 30141 + download_count: 30201 id: 10.5281/zenodo.5847355 license: CC-BY-4.0 links: [ilastik/covid_if_training_data, ilastik/ilastik, deepimagej/deepimagej, @@ -306,7 +306,7 @@ 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: 29988 + download_count: 30102 id: 10.5281/zenodo.6406803 license: CC-BY-4.0 links: [deepimagej/deepimagej, ilastik/ilastik, imjoy/BioImageIO-Packager, ilastik/torch-em-2d-unet-notebook] @@ -327,7 +327,7 @@ 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: 29565 + download_count: 29696 id: 10.5281/zenodo.5817052 license: MIT links: [imjoy/BioImageIO-Packager, zero/notebook_u-net_2d_zerocostdl4mic_deepimagej, @@ -348,7 +348,7 @@ collection: created: '2023-03-02 05:53:45.695883' description: Nuclei segmentation model for segmenting images from the Human Protein Atlas - download_count: 28259 + download_count: 28325 id: 10.5281/zenodo.6200999 license: CC-BY-4.0 links: [deepimagej/deepimagej] @@ -368,7 +368,7 @@ 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: 27401 + download_count: 27465 id: 10.5281/zenodo.6384845 license: MIT links: [deepimagej/deepimagej, imjoy/BioImageIO-Packager] @@ -390,7 +390,7 @@ 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: 26140 + download_count: 26204 id: 10.5281/zenodo.6383429 license: MIT links: [deepimagej/deepimagej, imjoy/BioImageIO-Packager] @@ -412,7 +412,7 @@ 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: 24837 + download_count: 24950 id: 10.5281/zenodo.7261974 license: MIT links: [deepimagej/deepimagej, imjoy/BioImageIO-Packager, zero/dataset_u-net_2d_multilabel_deepbacs, @@ -434,7 +434,7 @@ 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: 24262 + download_count: 24362 id: 10.5281/zenodo.6079314 license: CC-BY-4.0 links: [imjoy/BioImageIO-Packager, ilastik/torch-em-2d-unet-notebook, ilastik/ilastik, @@ -453,7 +453,7 @@ 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: 23957 + download_count: 24021 id: 10.5281/zenodo.6334383 license: MIT links: [imjoy/BioImageIO-Packager] @@ -474,7 +474,7 @@ 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: 21891 + download_count: 21955 id: 10.5281/zenodo.6334881 license: MIT links: [imjoy/BioImageIO-Packager] @@ -495,7 +495,7 @@ 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: 21297 + download_count: 21338 id: 10.5281/zenodo.6334777 license: MIT links: [deepimagej/deepimagej, imjoy/BioImageIO-Packager] @@ -514,7 +514,7 @@ 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: 21147 + download_count: 21234 id: 10.5281/zenodo.5910854 license: MIT links: [imjoy/BioImageIO-Packager, hpa/hpa-kaggle-2021-dataset] @@ -535,7 +535,7 @@ 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: 20334 + download_count: 20390 id: 10.5281/zenodo.6334583 license: MIT links: [imjoy/BioImageIO-Packager] @@ -553,7 +553,7 @@ 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: 19461 + download_count: 19571 id: 10.5281/zenodo.6811491 license: CC-BY-4.0 links: [deepimagej/deepimagej, ilastik/torch-em-3d-unet-notebook, ilastik/ilastik, @@ -574,7 +574,7 @@ 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: 18834 + download_count: 18842 id: 10.5281/zenodo.6865412 license: CC-BY-4.0 name: Cells and gland Segmentation (FRUNet) @@ -590,7 +590,7 @@ 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: 18385 + download_count: 18417 id: 10.5281/zenodo.5910163 license: MIT links: [imjoy/BioImageIO-Packager] @@ -613,7 +613,7 @@ 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: 17174 + download_count: 17298 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 @@ -633,7 +633,7 @@ 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: 14196 + download_count: 14282 id: 10.5281/zenodo.6808325 license: CC-BY-4.0 links: [ilastik/ilastik, deepimagej/deepimagej, ilastik/torch-em-3d-unet-notebook, @@ -652,7 +652,7 @@ 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: 13619 + download_count: 13708 id: 10.5281/zenodo.7274275 license: CC-BY-4.0 links: [deepimagej/deepimagej] @@ -675,7 +675,7 @@ 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: 10349 + download_count: 10387 id: 10.5281/zenodo.7315440 license: GPL-3.0 links: [Embryonet.de, imjoy/BioImageIO-Packager] @@ -695,7 +695,7 @@ 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: 9476 + download_count: 9539 id: 10.5281/zenodo.7380171 license: CC-BY-4.0 name: Drosophila epithelia cell boundary segmentation of 2D projections @@ -714,7 +714,7 @@ 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: 9188 + download_count: 9246 id: 10.5281/zenodo.7772662 license: MIT links: [imjoy/BioImageIO-Packager] @@ -733,7 +733,7 @@ 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: 8823 + download_count: 8909 id: 10.5281/zenodo.7614645 license: MIT links: [imjoy/BioImageIO-Packager] @@ -756,7 +756,7 @@ 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: 6565 + download_count: 6625 id: 10.5281/zenodo.7786492 license: MIT links: [deepimagej/deepimagej, imjoy/BioImageIO-Packager] @@ -780,7 +780,7 @@ 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: 6235 + download_count: 6237 download_url: https://cbia.fi.muni.cz/files/segmentation/fru-net/FRU_processing.zip id: 10.5281/zenodo.6559929 license: MIT @@ -805,7 +805,7 @@ 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: 4128 + download_count: 4180 id: 10.5281/zenodo.8421755 license: CC-BY-4.0 links: [imjoy/BioImageIO-Packager] @@ -824,7 +824,7 @@ 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: 4010 + download_count: 4060 id: 10.5281/zenodo.8064806 license: Apache-2.0 links: [imjoy/BioImageIO-Packager] @@ -846,7 +846,7 @@ collection: created: '2023-10-09 06:57:28.189519' description: Pre-training a Foundation Model for Universal Fluorescence Microscopy Image Restoration - download_count: 3000 + download_count: 3040 id: 10.5281/zenodo.8419845 license: CC-BY-4.0 name: UniFMIRSuperResolutionOnMicrotubules @@ -867,7 +867,7 @@ collection: created: '2023-10-09 07:05:52.763368' description: Pre-training a Foundation Model for Universal Fluorescence Microscopy Image Restoration - download_count: 2354 + download_count: 2391 id: 10.5281/zenodo.8420099 license: CC-BY-4.0 links: [imjoy/BioImageIO-Packager] @@ -886,7 +886,7 @@ 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: 2119 + download_count: 2120 id: 10.5281/zenodo.7612115 license: MIT name: Hatchling Medaka Heart (HyLFM) @@ -902,7 +902,7 @@ 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: 1753 + download_count: 1755 id: 10.5281/zenodo.8142283 license: MIT links: [imjoy/BioImageIO-Packager] @@ -927,7 +927,7 @@ 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: 1377 + download_count: 1380 id: 10.5281/zenodo.8401064 license: CC-BY-4.0 links: [imjoy/BioImageIO-Packager]