Repositories list

• W_NucleiSegmentation-Cellpose

  Public template
  Python

  •

  Apache License 2.0

  •1•0•2•0•Updated Sep 7, 2023Sep 7, 2023

• presentations

  Public
  Presentations about biaflows

  Creative Commons Zero v1.0 Universal

  •0•1•0•0•Updated May 9, 2023May 9, 2023

• W_NucleiSegmentation3D-ImageJ

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

  Dockerfile

  •1•2•0•0•Updated May 9, 2023May 9, 2023

• neubias-wg5.github.io

  Public
  HTML

  •0•0•0•0•Updated May 8, 2023May 8, 2023

• W_ObjectTracking-MU-Lux-CZ

  Public template
  Python

  •1•2•0•0•Updated Oct 22, 2022Oct 22, 2022

• W_PixCla-PSPNet-GlaS

  Public template
  BIAFLOWS workflow using neural network PSPNet on GlaS dataset

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Oct 22, 2022Oct 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.

  Dockerfile

  •0•0•0•0•Updated Oct 22, 2022Oct 22, 2022

• W_LandmarkDetect-ML-MSET-Pred

  Public template
  Python

  •0•0•0•0•Updated Oct 22, 2022Oct 22, 2022

• W_PixCla-UNet-GlaS

  Public template
  Pixel classification for GlaS challenge with UNet

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Oct 22, 2022Oct 22, 2022

• W_NucleiSegmentation3D-ilastik

  Public template
  BIAFLOWS workflow for 3D nuclei segmentation in ilastik.

  Python

  •0•0•0•0•Updated Oct 22, 2022Oct 22, 2022

• W_LandmarkDetect-ML-LC-Pred

  Public template
  Python

  •0•0•0•0•Updated Oct 22, 2022Oct 22, 2022

• W_NucleiSegmentation-Sandbox

  Public template
  BIAFLOWS Sandbox workflow.

  Dockerfile

  •0•0•0•0•Updated Oct 22, 2022Oct 22, 2022

• W_SpotDetection3D-Icy

  Public template
  BIAFLOWS workflow using a 3D spot detection protocol from Icy .

  JavaScript

  •0•0•0•0•Updated Oct 22, 2022Oct 22, 2022

• W_NucleiSegmentation-DeepCell

  Public template
  BIAFLOWS nuclei segmentation workflow using DeepCell 1.0.

  Python

  •1•0•0•0•Updated Oct 22, 2022Oct 22, 2022

• W_FilamentTracing3D-ImageJ

  Public template
  FilamentTracing3D-ImageJ

  Python

  •0•0•0•0•Updated Oct 22, 2022Oct 22, 2022

• W_FilamentTracing3D-Tub-IJ

  Public template
  Python

  •0•0•0•0•Updated Oct 22, 2022Oct 22, 2022

• W_LogPartTrack_IJ

  Public template
  Particle tracking based on linking closest intensity minima detected from LoG filtered time-lapse

  ImageJ Macro

  •0•0•0•0•Updated Oct 22, 2022Oct 22, 2022

• W_ObjectTracking-PAST-FR

  Public template
  A neubias software for object tracking using PAST FR method

  ImageJ Macro

  •

  Apache License 2.0

  •0•0•0•0•Updated Oct 22, 2022Oct 22, 2022

• W_NucleiSegmentation-MaskRCNN

  Public template
  NEUBIAS-WG5 workflow for nuclei segmentation using Mask-RCNN

  Python

  •0•1•0•0•Updated Oct 22, 2022Oct 22, 2022

• W_NeuronTracing_vaa3d_app2

  Public template
  BIAFLOWS workflow for neuron and tree 3d segmentation using all-path-pruning 2.0 (APP2) of Vaa3D

  Python

  •0•0•0•0•Updated Oct 22, 2022Oct 22, 2022

• W_NucleiSegmentation-ilastik

  Public template
  BIAFLOWS workflow for nuclei segmentation using ilastik and Python.

  Python

  •0•0•0•0•Updated Oct 22, 2022Oct 22, 2022

• W_LandmarkDetect-ML-MSET-Train

  Public template
  Python

  •0•0•0•0•Updated Oct 22, 2022Oct 22, 2022

• W_SpotDetection-IJ

  Public template
  Spot detection in FIJI using a LoG filter and the detection of minima

  Dockerfile

  •0•0•0•0•Updated Oct 22, 2022Oct 22, 2022

• W_SpotDetection-Dmap-IJ

  Public template
  Distance map based spot detection ImageJ macro

  Dockerfile

  •0•0•0•0•Updated Oct 22, 2022Oct 22, 2022

• W_ObjectTracking-Octave

  Public template
  Nuclei tracking in 2D time-lapse with Octave tracker (adapted from Matlab LOBSTER version: https://github.com/SebastienTs/LOBSTER)

  MATLAB

  •

  Apache License 2.0

  •0•0•0•0•Updated Oct 22, 2022Oct 22, 2022

• W_Neuron3dTree_vaa3d_most

  Public template
  BIAFLOWS workflow for tree 3d segmentation using MOST Vessel Tracer of Vaa3D

  Python

  •0•1•0•0•Updated Oct 22, 2022Oct 22, 2022

• W_PartTracking-ImageJ

  Public template
  Particle tracking based on linking closest intensity minima detected from LoG filtered time-lapse

  ImageJ Macro

  •0•0•0•0•Updated Oct 22, 2022Oct 22, 2022

• W_FilamentTracing3D-LocThr-IJ

  Public template
  Python

  •0•0•0•0•Updated Oct 22, 2022Oct 22, 2022

• W_LandmarkDetect-ML-DMBL-Pred

  Public template
  Python

  •0•0•0•0•Updated Oct 22, 2022Oct 22, 2022

• W_NucleiSegmentation-CellProfiler

  Public template
  NEUBIAS-WG5 workflow for nuclei segmentation using CellProfiler 2.2.0

  Python

  •2•2•2•0•Updated Oct 22, 2022Oct 22, 2022