Workflow

A workflow is a set of components assembled in some specific order to

  1. Measure and estimate some numerical parameters of the biological system or
  2. Visualization

for addressing a biological question. Workflows can be a combination of components from the same or different software packages using several scripts and manual steps.

3D Nuclei Clustering Tool

Workflow
Description

Analyze the clustering behavior of nuclei in 3D images. The centers of the nuclei are detected. The nuclei are filtered by the presence of a signal in a different channel. The clustering is done with the density based algorithm DBSCAN. The nearest neighbor distances between all nuclei and those outside and inside of the clusters are calculated.

has topic
Fluorescence microscopy
has function
Clustering

Neuron Tracing Vaa3D (BJUT FM Spanning Tree)

Workflow
Description

Vaa3d BJUT Fast Marching Spanning Tree algorithm dockerised workflow for BIAFLOWS

has topic
Bioimage informatics
has function
Filament tracing
Neuron image analysis
need a thumbnail

Filament Tracing LocThresh (ImageJ)

Workflow
Description

Blood vessels tracing in 3D image from 3D Gaussian blurring (user defined radius), local thresholding (user defined radius and offset) and 3D skeletonization. Dockerized version for BIAFLOWS,

has topic
Bioimage informatics
has function
Filament tracing
Local thresholding
Skeletonisation
need a thumbnail

Filament Tracing Tubeness (ImageJ)

Workflow
Description

Blood vessels tracing in 3D image from Tubeness filtering (user defined scale), 3D opening (radius set to 2), thresholding (user defined level) and 3D skeletonization.

has topic
Bioimage informatics
has function
Filament tracing
Image segmentation
Feature enhancement
Skeletonisation
need a thumbnail
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