From 80eb0a062eff7ef39ce20143b155fdc70dd4ab46 Mon Sep 17 00:00:00 2001 From: FynnBe Date: Fri, 10 Nov 2023 03:24:56 +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 ccad77aa6..7ca2b41ce 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": 45348, + "download_count": 45532, "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": 33964, + "download_count": 33985, "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": 33105, + "download_count": 33174, "id": "10.5281/zenodo.5869899", "license": "CC-BY-4.0", "links": [ @@ -157,7 +157,7 @@ ], "created": "2022-02-09 21:14:46.430029", "description": "{organelle} segmentation in EM of platynereis.", - "download_count": 30818, + "download_count": 30871, "id": "10.5281/zenodo.6028097", "license": "CC-BY-4.0", "links": [ @@ -200,7 +200,7 @@ ], "created": "2022-06-10 06:22:28.465944", "description": "Mitochondria segmentation for electron microscopy.", - "download_count": 30731, + "download_count": 30809, "id": "10.5281/zenodo.5874841", "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": 30098, + "download_count": 30103, "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": 28826, + "download_count": 28879, "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": 27692, + "download_count": 27793, "id": "10.5281/zenodo.5914248", "license": "BSD-2-Clause", "links": [ @@ -392,7 +392,7 @@ ], "created": "2023-03-06 19:01:04.321374", "description": "Cell segmentation model for segmenting images from the Human Protein Atlas", - "download_count": 27348, + "download_count": 27368, "id": "10.5281/zenodo.6200635", "license": "CC-BY-4.0", "links": [ @@ -439,7 +439,7 @@ ], "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": 27243, + "download_count": 27323, "id": "10.5281/zenodo.5749843", "license": "MIT", "links": [ @@ -491,7 +491,7 @@ ], "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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Voxel size: (0.235, 0.150, 0.150) microns ZYX", - "download_count": 17404, + "download_count": 17425, "id": "10.5281/zenodo.6334583", "license": "MIT", "links": [ @@ -1178,7 +1178,7 @@ ], "created": "2022-07-28 07:37:36.393648", "description": "DeepImageJ compatible FRUNet trained to subtly segment cells and gland.", - "download_count": 17332, + "download_count": 17348, "id": "10.5281/zenodo.6865412", "license": "CC-BY-4.0", "name": "Cells and gland Segmentation (FRUNet)", @@ -1214,7 +1214,7 @@ ], "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. (0.25x0.1625x0.1625) microns ZYX", - "download_count": 16851, + "download_count": 16897, "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": 16671, + "download_count": 16709, "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": 15226, + "download_count": 15261, "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": 15137, + "download_count": 15175, "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": 12693, + "download_count": 12762, "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": 10780, + "download_count": 10854, "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": 9621, + "download_count": 9646, "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": 8297, + "download_count": 8354, "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": 6550, + "download_count": 6554, "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": 6097, + "download_count": 6123, "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": 5984, + "download_count": 6002, "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": 5937, + "download_count": 5941, "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": 4539, + "download_count": 4565, "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": 3189, + "download_count": 3225, "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": 1973, + "download_count": 1975, "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": 1765, + "download_count": 1770, "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": 1269, + "download_count": 1273, "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": 671, + "download_count": 706, "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": 559, + "download_count": 579, "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": 514, + "download_count": 520, "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": 281, + "download_count": 298, "id": "10.5281/zenodo.8420099", "license": "CC-BY-4.0", "links": [ diff --git a/rdf.yaml b/rdf.yaml index c8b524296..575f98d43 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: 45348 + download_count: 45532 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: 33964 + download_count: 33985 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: 33105 + download_count: 33174 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.6028097/6028098/cover.png'] created: '2022-02-09 21:14:46.430029' description: '{organelle} segmentation in EM of platynereis.' - download_count: 30818 + download_count: 30871 id: 10.5281/zenodo.6028097 license: CC-BY-4.0 links: [deepimagej/deepimagej, ilastik/ilastik, imjoy/BioImageIO-Packager, ilastik/torch-em-3d-unet-notebook] @@ -83,7 +83,7 @@ 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: 30731 + download_count: 30809 id: 10.5281/zenodo.5874841 license: CC-BY-4.0 links: [deepimagej/deepimagej, ilastik/ilastik, ilastik/mitoem_segmentation_challenge, @@ -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: 30098 + download_count: 30103 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: 28826 + download_count: 28879 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: 27692 + download_count: 27793 id: 10.5281/zenodo.5914248 license: BSD-2-Clause links: [imjoy/BioImageIO-Packager, deepimagej/deepimagej, ilastik/ilastik, deepimagej/unet-pancreaticcellsegmentation, @@ -166,7 +166,7 @@ collection: created: '2023-03-06 19:01:04.321374' description: Cell segmentation model for segmenting images from the Human Protein Atlas - download_count: 27348 + download_count: 27368 id: 10.5281/zenodo.6200635 license: CC-BY-4.0 links: [deepimagej/deepimagej, hpa/hpa-cell-image-segmentation-dataset, imjoy/BioImageIO-Packager, @@ -187,7 +187,7 @@ 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: 27243 + download_count: 27323 id: 10.5281/zenodo.5749843 license: MIT links: [imjoy/BioImageIO-Packager, ilastik/ilastik, deepimagej/deepimagej, zero/notebook_u-net_3d_zerocostdl4mic] @@ -210,7 +210,7 @@ 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: 26664 + download_count: 26705 id: 10.5281/zenodo.6346511 license: MIT links: [deepimagej/deepimagej, imjoy/BioImageIO-Packager, ilastik/ilastik] @@ -230,7 +230,7 @@ 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: 26607 + download_count: 26653 id: 10.5281/zenodo.6348084 license: BSD-3-Clause links: [deepimagej/deepimagej, imjoy/BioImageIO-Packager, bioimageio/stardist, bioimageio/qupath, @@ -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: 26589 + download_count: 26652 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: 25001 + download_count: 25070 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: 24965 + download_count: 25024 id: 10.5281/zenodo.5847355 license: CC-BY-4.0 links: [ilastik/covid_if_training_data, ilastik/ilastik, deepimagej/deepimagej, @@ -308,7 +308,7 @@ collection: created: '2023-03-02 05:53:45.695883' description: Nuclei segmentation model for segmenting images from the Human Protein Atlas - download_count: 23348 + download_count: 23410 id: 10.5281/zenodo.6200999 license: CC-BY-4.0 links: [deepimagej/deepimagej, ilastik/ilastik] @@ -328,7 +328,7 @@ 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: 23249 + download_count: 23331 id: 10.5281/zenodo.5817052 license: MIT links: [imjoy/BioImageIO-Packager, zero/notebook_u-net_2d_zerocostdl4mic_deepimagej, @@ -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: 23011 + download_count: 23067 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: 21895 + download_count: 21939 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: 21083 + download_count: 21142 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: 20760 + download_count: 20780 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: 19215 + download_count: 19269 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: 18722 + download_count: 18738 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: 17404 + download_count: 17425 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: 17332 + download_count: 17348 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: 16851 + download_count: 16897 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: 16671 + download_count: 16709 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: 15226 + download_count: 15261 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: 15137 + download_count: 15175 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: 12693 + download_count: 12762 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: 10780 + download_count: 10854 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: 9621 + download_count: 9646 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: 8297 + download_count: 8354 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: 6550 + download_count: 6554 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: 6097 + download_count: 6123 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: 5984 + download_count: 6002 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: 5937 + download_count: 5941 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: 4539 + download_count: 4565 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: 3189 + download_count: 3225 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: 1973 + download_count: 1975 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: 1765 + download_count: 1770 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: 1269 + download_count: 1273 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: 671 + download_count: 706 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: 559 + download_count: 579 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: 514 + download_count: 520 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: 281 + download_count: 298 id: 10.5281/zenodo.8420099 license: CC-BY-4.0 links: [imjoy/BioImageIO-Packager]