manifest.bioimage.io.yaml

format_version: 0.2.2
type: collection
name: HPA Collection
tags: [hpa, bioimage.io]
description: "Resources for BioImgage.IO curated by the the cellprofiling group at HPA."
config:
  id: hpa
  name: HPA
  tags:
    - hpa
  logo: >-
    https://raw.githubusercontent.com/bioimage-io/tfjs-bioimage-io/master/apps/hpa-logo.gif
  icon: >-
    https://raw.githubusercontent.com/bioimage-io/tfjs-bioimage-io/master/apps/hpa-logo.gif
  about_url: https://www.proteinatlas.org/
  splash_title: The Human Protein Atlas
  splash_subtitle: null
  splash_feature_list: []
  explore_button_text: Start Exploring
  background_image: static/img/zoo-background.svg
  resource_types:
    - model
    - application
  default_type: model
  docs: https://www.proteinatlas.org/about
  contact:
    - name: Frederic Ballllosera Navarro
      email: fredbn@stanford.edu
      github: OmFrederic
      affiliation:
        - name: KTH
          url: https://kth.se
        - name: Stanford
          url: https://stanford.edu
collection:
  - id: HPA-Classification
    type: application
    documentation: https://raw.githubusercontent.com/CellProfiling/HPA-model-zoo/master/collection/hpa-classification-app.md
    source: >-
      https://raw.githubusercontent.com/imjoy-team/imjoy-plugins/master/repository/HPA-Classification.imjoy.html
#   - id: HPAShuffleNetV2
#     type: model
#     rdf_source: >-
#       https://raw.githubusercontent.com/bioimage-io/tfjs-bioimage-io/master/models/HPAShuffleNetV2/HPAShuffleNetV2.model.yaml
#     links:
#       - HPA-Classification
  - id: hpa-cell-image-segmentation-dataset
    authors:
    - {name: Jay Kaimal}
    - {name: Peter Thul}
    - {name: Hao Xu}
    - {name: Wei Ouyang}
    - {name: Emma Lundberg}
    cite:
    - {doi: 'https://doi.org/10.5281/zenodo.4665863', text: 'Kaimal et al.'}
    covers: ['https://zenodo.org/api/files/a24a1e8a-cdc5-4b56-b9c3-0b82417e74a5/hpaseg-cover.png']
    description: Annotated images from the Human Protein Atlas for cell segmentation
    documentation: https://raw.githubusercontent.com/CellProfiling/HPA-model-zoo/master/collection/hpa-cell-image-segmentation-dataset.md
    format_version: 0.2.1
    license: CC-BY-4.0
    name: HPA Cell Image Segmentation Dataset
    source: https://zenodo.org/record/4665863
    tags: [fluorescence-light-microscopy, 2D, cells, nuclei, semantic-segmentation, instance-segmentation]
    download_url: https://zenodo.org/record/4665863/files/hpa_cell_segmentation_dataset_v2_512x512_4train_159test.zip?download=1
    type: dataset
  - id: hpa-kaggle-2021-dataset
    authors:
    - {name: The Human Protein Atlas}
    cite: []
    covers: ['https://raw.githubusercontent.com/CellProfiling/HPA-model-zoo/master/collection/hpa-single-cell-classification.png']
    description: Training dataset for the Human Protein Atlas Single Cell Classification competition 2021
    documentation: https://raw.githubusercontent.com/CellProfiling/HPA-model-zoo/master/collection/hpa-single-cell-classification.md
    format_version: 0.2.1
    license: CC-BY-4.0
    name: HPA Single Cell Classification Dataset 2021
    source: https://www.kaggle.com/competitions/hpa-single-cell-image-classification/data
    tags: [fluorescence-light-microscopy, 2D, cells, nuclei, protein, classification]
    download_url: https://www.kaggle.com/competitions/hpa-single-cell-image-classification/data
    type: dataset
#   - id: HPA-bestfitting
#     type: model
#     name: HPA-bestfitting
#     tags:
#       - classification
#       - densenet-121
#       - inception-v3
#       - resnet-34
#       - resnet-50
#     framework: pytorch
#     authors:
#       - Shubin Dai
#     license: MIT
#     cite: null
#     git_repo: >-
#       https://github.com/CellProfiling/HPA-competition-solutions/tree/master/bestfitting
#     description: >-
#       A CNN model using focal loss and image augmentation, optimized with Adam
#       optimizer.
#     documentation: >-
#       https://raw.githubusercontent.com/CellProfiling/HPA-competition-solutions/master/bestfitting/README.md
#     badges:
#       - label: HPA Competition
#         ext: 1st
#         url: https://www.kaggle.com/c/human-protein-atlas-image-classification/leaderboard
#     covers:
#       - https://raw.githubusercontent.com/CellProfiling/HPA-model-zoo/master/hpa_challenge_header.png
#       - https://raw.githubusercontent.com/CellProfiling/HPA-competition-solutions/master/bestfitting/src/bestfitting-densenet-diagram.png
#   - id: HPA-WAIR
#     type: model
#     name: HPA-WAIR
#     tags:
#       - classification
#       - densenet-121
#       - densenet-169
#       - ibn-densenet-121
#       - opencv
#       - scikit-learn
#       - se-resnext-50
#       - xception
#     framework: pytorch
#     authors:
#       - Jun Lan
#     license: MIT
#     git_repo: >-
#       https://github.com/CellProfiling/HPA-competition-solutions/tree/master/wair
#     description: >-
#       Seven CNN models, using multiple different architectures, ensembled
#       through averaging.
#     documentation: >-
#       https://raw.githubusercontent.com/CellProfiling/HPA-competition-solutions/master/wair/README.md
#     badges:
#       - label: HPA Competition
#         ext: 2nd
#         url: https://www.kaggle.com/c/human-protein-atlas-image-classification/leaderboard
#     covers:
#       - https://raw.githubusercontent.com/CellProfiling/HPA-model-zoo/master/hpa_challenge_header.png
#   - id: HPA-pudae
#     type: model
#     name: HPA-pudae
#     tags:
#       - classification
#       - inception-v3
#       - resnet-34
#       - se-resnext-50
#     framework: pytorch
#     authors:
#       - Park Jinmo
#     license: BSD-2-Clause
#     git_repo: 'https://github.com/CellProfiling/pudae-kaggle-hpa'
#     description: >-
#       An ensemble using focal loss, per image normalization and spatial
#       attention.
#     documentation: >-
#       https://raw.githubusercontent.com/CellProfiling/pudae-kaggle-hpa/master/README.md
#     badges:
#       - label: HPA Competition
#         ext: 3rd
#         url: https://www.kaggle.com/c/human-protein-atlas-image-classification/leaderboard
#     covers:
#       - https://raw.githubusercontent.com/CellProfiling/HPA-model-zoo/master/hpa_challenge_header.png
#   - id: HPA-wienerschnitzelgemeinschaft
#     type: model
#     name: HPA-wienerschnitzelgemeinschaft
#     tags:
#       - airnet-50
#       - airnext-50
#       - cbam
#       - classification
#       - hill-climbing
#       - inception-resnet-v2
#       - inception-v3
#       - preresnet-50
#       - resnet-18
#       - resnet-34
#       - resnet-50
#       - resnet-101
#       - se-resnext-50
#     framework: pytorch
#     authors:
#       - Shaikat Mahmood Galib
#       - Christof Henkel
#       - Kevin Hwang
#       - Dmytro Poplavskiy
#       - Bojan Tunguz
#       - Russ Wolfinger
#     license: MIT
#     git_repo: >-
#       https://github.com/CellProfiling/HPA-competition-solutions/tree/master/wienerschnitzelgemeinschaft
#     description: >-
#       An ensemble of diverse and highly optimized CNN models, using hill
#       climbing and weighted voting.
#     documentation: >-
#       https://raw.githubusercontent.com/CellProfiling/HPA-competition-solutions/master/wienerschnitzelgemeinschaft/README.md
#     badges:
#       - label: HPA Competition
#         ext: 4th
#         url: https://www.kaggle.com/c/human-protein-atlas-image-classification/leaderboard
#     covers:
#       - https://raw.githubusercontent.com/CellProfiling/HPA-model-zoo/master/hpa_challenge_header.png
#   - id: HPA-vpp
#     type: model
#     name: HPA-vpp
#     tags:
#       - classification
#       - inception-v3
#       - inception-v4
#       - multilayer-perceptron
#       - xception
#     framework: pytorch
#     authors:
#       - Yinzheng Gu
#       - Chuanpeng Li
#       - Jinbin Xie
#     license: MIT
#     git_repo: 'https://github.com/CellProfiling/HPA-competition-solutions/tree/master/vpp'
#     description: >-
#       An ensemble of seven CNN models and a multi-layer perceptron network,
#       using image augmentation, multi scales, weighted sampling and
#       MultiLabelSoftMargin loss.
#     documentation: >-
#       https://raw.githubusercontent.com/CellProfiling/HPA-competition-solutions/master/vpp/README.md
#     badges:
#       - label: HPA Competition
#         ext: 5th
#         url: https://www.kaggle.com/c/human-protein-atlas-image-classification/leaderboard
#     covers:
#       - https://raw.githubusercontent.com/CellProfiling/HPA-model-zoo/master/hpa_challenge_header.png
#   - id: HPA-One-More
#     type: model
#     name: HPA-One More Layer Of Stacking
#     tags:
#       - bn-inception
#       - classification
#       - inception-v4
#       - lightgbm
#       - se-resnext-50
#       - xception
#     framework: pytorch
#     authors:
#       - Dmitry Buslov
#       - Sergei Fironov
#       - Alexander Kiselev
#       - Dmytro Panchenko
#     license: MIT
#     git_repo: >-
#       https://github.com/CellProfiling/HPA-competition-solutions/tree/master/one_more_layer_of_stacking
#     description: >-
#       14 CNN models ensembled via LightGBM stacking, optimized with Wadam, using
#       focal and LSEP loss.
#     documentation: >-
#       https://raw.githubusercontent.com/CellProfiling/HPA-competition-solutions/master/one_more_layer_of_stacking/README.md
#     badges:
#       - label: HPA Competition
#         ext: 8th
#         url: https://www.kaggle.com/c/human-protein-atlas-image-classification/leaderboard
#     covers:
#       - https://raw.githubusercontent.com/CellProfiling/HPA-model-zoo/master/hpa_challenge_header.png
#   - id: HPA-conv
#     type: model
#     name: HPA-conv is all you need
#     tags:
#       - classification
#       - inception-v3
#       - se-resnext-50
#       - xception
#     framework: pytorch
#     authors:
#       - Xuan Cao
#       - Runmin Wei
#       - Yuanhao Wu
#       - Xun Zhu
#     license: MIT
#     git_repo: >-
#       https://github.com/CellProfiling/HPA-competition-solutions/tree/master/conv_is_all_you_need
#     description: >-
#       An ensemble of a cropping window CNN based on Xception, and two
#       conventional CNNs based on SE-ResNext50 and InceptionV3.
#     documentation: >-
#       https://raw.githubusercontent.com/CellProfiling/HPA-competition-solutions/master/conv_is_all_you_need/README.md
#     badges:
#       - label: HPA Competition
#         ext: 10th
#         url: https://www.kaggle.com/c/human-protein-atlas-image-classification/leaderboard
#     covers:
#       - https://raw.githubusercontent.com/CellProfiling/HPA-model-zoo/master/hpa_challenge_header.png
#   - id: HPA-NTU_MiRA
#     type: model
#     name: HPA-NTU_MiRA
#     tags:
#       - classification
#       - resnet-34
#     framework: tensorflow
#     authors:
#       - Kuan-Lun Tseng
#     license: MIT
#     git_repo: >-
#       https://github.com/CellProfiling/HPA-competition-solutions/tree/master/ntu_mira
#     description: >-
#       A CNN with large input size (1024 ⨉ 1024 px) using fixed
#       batch-normalization and data distillation.
#     documentation: >-
#       https://raw.githubusercontent.com/CellProfiling/HPA-competition-solutions/master/ntu_mira/README.md
#     badges:
#       - label: HPA Competition
#         ext: 16th
#         url: https://www.kaggle.com/c/human-protein-atlas-image-classification/leaderboard
#     covers:
#       - https://raw.githubusercontent.com/CellProfiling/HPA-model-zoo/master/hpa_challenge_header.png
#   - id: HPA-Random-Walk
#     type: model
#     name: HPA-Random Walk
#     tags:
#       - attention-gate
#       - classification
#       - resnet-18
#     framework: pytorch
#     authors:
#       - Zhifeng Gao
#       - Cheng Ju
#       - Xiaohan Yi
#       - Hongdong Zheng
#     license: MIT
#     git_repo: >-
#       https://github.com/CellProfiling/HPA-competition-solutions/tree/master/random_walk
#     description: >-
#       An ensemble model of three different resolutions based on single attention
#       gated network.
#     documentation: >-
#       https://raw.githubusercontent.com/CellProfiling/HPA-competition-solutions/master/random_walk/README.md
#     badges:
#       - label: HPA Competition
#         ext: 38th
#         url: https://www.kaggle.com/c/human-protein-atlas-image-classification/leaderboard
#     covers:
#       - https://raw.githubusercontent.com/CellProfiling/HPA-model-zoo/master/hpa_challenge_header.png