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@Neubias-WG5

Biaflows / Neubias-WG5

A collaborative framework based on Cytomine to benchmark and deploy bioimage analysis workflows. The project is supported by NEUBIAS COST ACTION CA15124

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  1. W_NucleiSegmentation-CellProfiler W_NucleiSegmentation-CellProfiler Public template

    NEUBIAS-WG5 workflow for nuclei segmentation using CellProfiler 2.2.0

    Python 2 2

  2. W_NucleiSegmentation3D-ImageJ W_NucleiSegmentation3D-ImageJ Public template

    BIAFLOWS workflow to segment clustered nuclei using a 3D filter, thresholding and a 3D binary watershed.

    Dockerfile 2 1

  3. W_NucleiSegmentation-UNet W_NucleiSegmentation-UNet Public template

    3-class U-Net segmentation.

    Python 2 1

  4. W_ObjectTracking-MU-Lux-CZ W_ObjectTracking-MU-Lux-CZ Public template

    Python 2 1

  5. W_NeuronTracing_vaa3d_fastmarching_spanningtree W_NeuronTracing_vaa3d_fastmarching_spanningtree Public template

    Trace 3d neuron with vaa3d BJUT Fast Marching Spanning Tree algorithm

    Python 2

  6. Biaflows-bootstrap Biaflows-bootstrap Public

    Forked from Cytomine-ULiege/Cytomine-bootstrap

    Biaflows installation procedure on a web server or a personal laptop. This procedure is based on ULiege Cytomine bootstrap (see @cytomine-uliege & @cytomine).

    Shell 1 1

Repositories

Showing 10 of 85 repositories
  • W_NucleiSegmentation-Cellpose Public template
    Neubias-WG5/W_NucleiSegmentation-Cellpose’s past year of commit activity
    Python 0 Apache-2.0 1 2 0 Updated Sep 7, 2023
  • presentations Public

    Presentations about biaflows

    Neubias-WG5/presentations’s past year of commit activity
    1 CC0-1.0 0 0 0 Updated May 9, 2023
  • W_NucleiSegmentation3D-ImageJ Public template

    BIAFLOWS workflow to segment clustered nuclei using a 3D filter, thresholding and a 3D binary watershed.

    Neubias-WG5/W_NucleiSegmentation3D-ImageJ’s past year of commit activity
    Dockerfile 2 1 0 0 Updated May 9, 2023
  • neubias-wg5.github.io Public
    Neubias-WG5/neubias-wg5.github.io’s past year of commit activity
    HTML 0 0 0 0 Updated May 8, 2023
  • W_ObjectTracking-MU-Lux-CZ Public template
    Neubias-WG5/W_ObjectTracking-MU-Lux-CZ’s past year of commit activity
    Python 2 1 0 0 Updated Oct 22, 2022
  • W_PixCla-PSPNet-GlaS Public template

    BIAFLOWS workflow using neural network PSPNet on GlaS dataset

    Neubias-WG5/W_PixCla-PSPNet-GlaS’s past year of commit activity
    Python 0 Apache-2.0 0 0 0 Updated Oct 22, 2022
  • W_NucleiTracking-ImageJ Public template

    BIAFLOWS workflow to track nuclei in a time series. The tracking uses a 3D-object segmentation with watershed to track the nuclei.

    Neubias-WG5/W_NucleiTracking-ImageJ’s past year of commit activity
    Dockerfile 0 0 0 0 Updated Oct 22, 2022
  • W_LandmarkDetect-ML-MSET-Pred Public template
    Neubias-WG5/W_LandmarkDetect-ML-MSET-Pred’s past year of commit activity
    Python 0 0 0 0 Updated Oct 22, 2022
  • W_PixCla-UNet-GlaS Public template

    Pixel classification for GlaS challenge with UNet

    Neubias-WG5/W_PixCla-UNet-GlaS’s past year of commit activity
    Python 0 Apache-2.0 0 0 0 Updated Oct 22, 2022
  • W_NucleiSegmentation3D-ilastik Public template

    BIAFLOWS workflow for 3D nuclei segmentation in ilastik.

    Neubias-WG5/W_NucleiSegmentation3D-ilastik’s past year of commit activity
    Python 0 0 0 0 Updated Oct 22, 2022
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