Workflow | BIII

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

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

Bioimage analysis with Icy

Short description

This webinar is part the serie of webinars from the NEUBIAS Academy @home

Recording: https://www.youtube.com/watch?v=5SJqhKjCbMQ&feature=youtu.be .

Slides: https://marionlouveaux.github.io/bioimage_analysis_with_icy/

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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

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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

has function

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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

has function