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seg_methods.js
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seg_methods.js
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export default {
'seg_methods': [
{
m_id: 0,
m_name: 'U-Net',
m_author: 'Ronneberger et al.',
m_year: '2015',
m_journal: 'MICCAI 2015',
m_links:{
m_code: 'https://github.com/zhixuhao/unet',
m_paper: 'http://dx.doi.org/10.1007/978-3-319-24574-4_28',
m_cites: 'https://scholar.google.com/scholar?hl=en&as_sdt=2005&sciodt=0%2C5&cites=10845403114495995712&scipsc=1&q=&btnG=',
m_pretrained:[
{
m_pr_id: '21',
m_pr_name: 'Pretrained phase-contrast model',
m_link: 'https://lmb.informatik.uni-freiburg.de/people/ronneber/u-net/'
},
{
m_pr_id: '20',
m_pr_name: 'Pretrained model for DIC',
m_link: 'https://lmb.informatik.uni-freiburg.de/people/ronneber/u-net/'
},
{
m_pr_id: '17',
m_pr_name: 'Pretrained fluorescent model',
m_link: 'https://github.com/carpenterlab/2019_caicedo_cytometryA.git'
},
{
m_pr_id: null,
m_pr_name: 'AnnotatorJ model (general)',
m_link: 'https://github.com/spreka/annotatorj/releases/tag/v0.0.2-model'
},
{
m_pr_id: null,
m_pr_name: 'Pretrained U-Net by BIOMAG (general)',
m_link: 'https://drive.google.com/open?id=1lVJtS41vzMkIsCa3-i14mSmLBbaKazsq'
}
]
},
m_2d: true,
m_3d: false,
m_challenges: {
m_elongated: true,
m_concave: true,
m_deviating: true,
m_wobbling: true,
m_heterogen: true,
m_fragmented: true,
m_overlapping: true
}
}, {
m_id: 1,
m_name: 'Mask R-CNN',
m_author: 'He et al.',
m_year: '2017',
m_journal: 'ICCV 2017',
m_links:{
m_code: 'https://github.com/matterport/Mask_RCNN',
m_paper: 'https://doi.org/10.1109/ICCV.2017.322',
m_cites: 'https://scholar.google.com/scholar?hl=en&as_sdt=2005&sciodt=0%2C5&cites=11459229647356475672&scipsc=1&q=&btnG=',
m_pretrained:[
{
m_pr_id: null,
m_pr_name: 'DSB 2018 model (general)',
m_link: 'https://github.com/mirzaevinom/data_science_bowl_2018'
},
{
m_pr_id: null,
m_pr_name: 'Mask R-CNN pretrained by BIOMAG (general)',
m_link: 'https://drive.google.com/open?id=1lVJtS41vzMkIsCa3-i14mSmLBbaKazsq'
}
]
},
m_2d: true,
m_3d: false,
m_challenges: {
m_elongated: true,
m_concave: true,
m_deviating: true,
m_wobbling: true,
m_heterogen: true,
m_fragmented: true,
m_overlapping: true
}
}, {
m_id: 2,
m_name: 'StarDist',
m_author: 'Schmidt et al.',
m_year: '2018',
m_journal: 'MICCAI 2018 & WACV 2020)',
m_links:{
m_code: 'https://github.com/stardist/stardist',
m_paper: 'https://doi.org/10.1007/978-3-030-00934-2_30',
m_3D_paper: 'https://dx.doi.org/10.1109/WACV45572.2020.9093435',
m_cites: 'https://scholar.google.com/scholar?hl=en&as_sdt=2005&sciodt=0%2C5&cites=6261085790694927391&scipsc=1&q=&btnG=',
m_3D_cites: 'https://scholar.google.com/scholar?hl=en&as_sdt=2005&sciodt=0%2C5&cites=2139260067181824373&scipsc=1&q=&btnG=',
m_pretrained:[
{
m_pr_id: '17',
m_pr_name: 'Pretrained fluorescent model',
m_link: 'https://github.com/stardist/stardist/tree/master/models/paper/2D_dsb2018'
},
{
m_pr_id: '28',
m_pr_name: 'Pretrained H&E model',
m_link: 'https://github.com/stardist/stardist/tree/master/models/paper/2D_dsb2018'
},
{
m_pr_id: '3d',
m_pr_name: 'Pretrained 3d model',
m_link: 'https://github.com/stardist/stardist/tree/master/models/examples/3D_demo'
}
]
},
m_2d: true,
m_3d: true,
m_challenges: {
m_elongated: true,
m_concave: true,
m_deviating: true,
m_wobbling: true,
m_heterogen: true,
m_fragmented: true,
m_overlapping: true
}
}, {
m_id: 3,
m_name: 'nucleAIzer',
m_author: 'Hollandi et al.',
m_year: '2020',
m_journal: 'CellSyst',
m_links:{
m_code: 'https://github.com/spreka/biomagdsb',
m_paper: 'https://doi.org/10.1016/j.cels.2020.04.003',
m_site: 'http://nucleaizer.org/',
m_cites: 'https://scholar.google.com/scholar?hl=en&as_sdt=2005&sciodt=0%2C5&cites=4183125655597734419&scipsc=1&q=&btnG=',
m_pretrained:[
{
m_pr_id: null,
m_pr_name: 'Pretrained model (general)',
m_link: 'https://drive.google.com/open?id=1lVJtS41vzMkIsCa3-i14mSmLBbaKazsq'
}
]
},
m_2d: true,
m_3d: false,
m_challenges: {
m_elongated: true,
m_concave: true,
m_deviating: true,
m_wobbling: true,
m_heterogen: true,
m_fragmented: true,
m_overlapping: true
}
}, {
m_id: 4,
m_name: 'Cellpose',
m_author: 'Stringer et al.',
m_year: '2021',
m_journal: 'Nature Methods',
m_links:{
m_code: 'https://github.com/MouseLand/cellpose',
m_paper: 'https://doi.org/10.1038/s41592-020-01018-x',
m_site: 'https://www.cellpose.org',
m_cites: 'https://scholar.google.com/scholar?hl=en&as_sdt=2005&sciodt=0%2C5&cites=2743286584966802094&scipsc=1&q=&btnG=',
m_pretrained:[
{
m_pr_id: null,
m_pr_name: 'Nucleus model (general)',
m_link: ['https://www.cellpose.org/models/nuclei_0',
'https://www.cellpose.org/models/nuclei_1',
'https://www.cellpose.org/models/nuclei_2',
'https://www.cellpose.org/models/nuclei_3',
'https://www.cellpose.org/models/nucleitorch_0',
'https://www.cellpose.org/models/nucleitorch_1',
'https://www.cellpose.org/models/nucleitorch_2',
'https://www.cellpose.org/models/nucleitorch_3']
}
]
},
m_2d: true,
m_3d: true,
m_challenges: {
m_elongated: true,
m_concave: true,
m_deviating: true,
m_wobbling: true,
m_heterogen: true,
m_fragmented: true,
m_overlapping: true
}
}, {
m_id: 5,
m_name: 'UNet++',
m_author: 'Zhou et al.',
m_year: '2018',
m_journal: 'DLMIA 2018, ML-CDS 2018',
m_links:{
m_code: 'https://github.com/MrGiovanni/UNetPlusPlus',
m_paper: 'https://doi.org/10.1007/978-3-030-00889-5_1',
m_cites: 'https://scholar.google.com/scholar?hl=en&as_sdt=2005&sciodt=0%2C5&cites=3438577305591755991&scipsc=1&q=&btnG=',
m_pretrained: []
},
m_2d: true,
m_3d: false,
m_challenges: {
m_elongated: true,
m_concave: true,
m_deviating: true,
m_wobbling: true,
m_heterogen: true,
m_fragmented: true,
m_overlapping: true
}
}, {
m_id: 6,
m_name: 'MultiStar',
m_author: 'Walter et al.',
m_year: '2021',
m_journal: 'ISBI 2021',
m_links:{
m_code: 'https://github.com/overlapping-instances/MultiStar',
m_paper: 'https://doi.org/10.1109/ISBI48211.2021.9433769',
m_cites: 'https://scholar.google.com/scholar?hl=en&as_sdt=2005&sciodt=0%2C5&cites=7345388908580636549&scipsc=1&q=&btnG=',
m_pretrained: []
},
m_2d: true,
m_3d: false,
m_challenges: {
m_elongated: true,
m_concave: true,
m_deviating: true,
m_wobbling: true,
m_heterogen: true,
m_fragmented: true,
m_overlapping: true
}
}, {
m_id: 7,
m_name: 'CPN',
m_author: 'Upschulte et al.',
m_year: '2021',
m_journal: 'arXiv',
m_links:{
m_code: 'https://github.com/FZJ-INM1-BDA/celldetection',
m_paper: 'https://arxiv.org/abs/2104.03393',
m_cites: 'https://scholar.google.com/scholar?hl=en&as_sdt=2005&sciodt=0%2C5&cites=11779593445859050188&scipsc=1&q=&btnG=',
m_pretrained: []
},
m_2d: true,
m_3d: false,
m_challenges: {
m_elongated: true,
m_concave: true,
m_wobbling: true,
m_overlapping: true
}
}, {
m_id: 8,
m_name: 'HistomicsML2',
m_author: 'Lee et al.',
m_year: '2021',
m_journal: 'Cancer Research',
m_links:{
m_code: 'https://github.com/PathologyDataScience/HistomicsML2',
m_paper: 'https://doi.org/10.1158/0008-5472.CAN-20-0668',
m_cites: 'https://scholar.google.com/scholar?hl=en&as_sdt=2005&sciodt=0%2C5&cites=98287935443345053&scipsc=1&q=&btnG=',
m_pretrained: []
},
m_2d: true,
m_3d: false,
m_challenges: {
m_elongated: true,
m_concave: true
}
}, {
m_id: 9,
m_name: 'STORM',
m_author: 'Mela et al.',
m_year: '2021',
m_journal: 'BMC Bioinformatics',
m_links:{
m_code: 'https://github.com/YangLiuLab/Super-Resolution-Nuclei-Segmentation',
m_paper: 'https://doi.org/10.1186/s12859-021-04245-x',
m_cites: 'https://scholar.google.com/scholar?hl=en&as_sdt=2005&sciodt=0%2C5&cites=595912511406673690&scipsc=1&q=&btnG=',
m_pretrained:[
{
m_pr_id: '17',
m_pr_name: 'Pretrained fluorescent model',
m_link: 'https://drive.google.com/drive/folders/1yKxyXkk4ceXoDpd647i1_-JWLjzKOY7t?usp=sharing'
},
{
m_pr_id: '7',
m_pr_name: 'Pretrained fluorescent tissue model',
m_link: 'https://drive.google.com/drive/folders/1yKxyXkk4ceXoDpd647i1_-JWLjzKOY7t?usp=sharing'
}
]
},
m_2d: true,
m_3d: false,
m_challenges: {
m_elongated: true,
m_concave: true,
m_deviating: true,
m_wobbling: true,
m_heterogen: true,
m_fragmented: true,
m_overlapping: true
}
}, {
m_id: 10,
m_name: 'Vaa3D',
m_author: 'Peng et al.',
m_year: '2010',
m_journal: 'Nature Biotechnology',
m_links: {
m_code: 'https://github.com/Vaa3D/vaa3d_tools',
m_paper: 'https://doi.org/10.1038/nbt.1612',
m_site: 'http://vaa3d.org',
m_cites: 'https://scholar.google.com/scholar?hl=en&as_sdt=2005&sciodt=0%2C5&cites=3380503499651306453&scipsc=1&q=&btnG=',
m_pretrained: []
},
m_2d: false,
m_3d: true,
m_challenges: {
m_elongated: true,
m_concave: true,
m_deviating: false,
m_wobbling: false,
m_heterogen: false,
m_fragmented: false
}
}, {
m_id: 11,
m_name: 'IT3DImageJSuite',
m_author: 'Ollion et al.',
m_year: '2013',
m_journal: 'Bioinformatics',
m_links: {
m_code: 'https://imagejdocu.tudor.lu/plugin/stacks/3d_ij_suite/start',
m_paper: 'https://doi.org/10.1093/bioinformatics/btt276',
m_cites: 'https://scholar.google.com/scholar?hl=en&as_sdt=2005&sciodt=0%2C5&cites=15174242674682245726&scipsc=1&q=&btnG=',
m_pretrained: []
},
m_2d: false,
m_3d: true,
m_challenges: {
m_elongated: true,
m_concave: true,
m_deviating: true,
m_wobbling: false,
m_heterogen: false,
m_fragmented: false,
m_overlapping: false
}
}, {
m_id: 12,
m_name: 'LoS',
m_author: 'Asafi et al.',
m_year: '2013',
m_journal: 'Computer Graphics Forum',
m_links: {
m_code: 'https://www.physikalischebiologie.de/downloads',
m_paper: 'https://doi.org/10.1111/cgf.12169',
m_cites: 'https://scholar.google.com/scholar?hl=en&as_sdt=2005&sciodt=0%2C5&cites=14687221567883628747&scipsc=1&q=&btnG=',
m_pretrained: []
},
m_2d: false,
m_3d: true,
m_challenges: {
m_elongated: true,
m_concave: false,
m_deviating: false,
m_wobbling: false,
m_heterogen: true,
m_fragmented: false,
m_overlapping: true
}
}, {
m_id: 13,
m_name: 'OpenSegSPIM',
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