Neuron Tracing Vaa3D (BJUT FM Spanning Tree)

Description

Vaa3d BJUT Fast Marching Spanning Tree algorithm dockerised workflow for BIAFLOWS

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Filament Tracing LocThresh (ImageJ)

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,

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Filament Tracing Tubeness (ImageJ)

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.

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Neuron Tracing Vaa3D (MOST)

Description

3D Neuron Tracing with a Dockerized version of Vaa3D MOST Raytracer.

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Neuron Tracing Vaa3D (MST)

Description

3D Neuron Tracing using Dockerized version of Vaa3D Minimum Spanning Tree (MST).

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Neuron Tracing Vaa3D (App2)

Description

Vaa3d All-Path-Pruning 2.0 (APP2) dockerised workflow for BIAFLOWS.

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Nuclei Segmentation 3D (Ilastik)

Description

Execute Nuclei Segmentation in 3D images using pixel classification with ilastik.

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has function
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Spot Detection 3D Hessian (ImageJ)

Description

3D spot detection using the Determinant of Hessian (DoH) and the detection of 3D minima.

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Spot Detection 3D (Icy)

Description

Spot detection in 3D images by Wavelet Adaptive Threshold in Icy.

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NucleusJ

Description

Quote

Starting from image stacks, the nuclear boundary as well as nuclear bodies are segmented. As output, NucleusJ automatically measures 15 parameters quantifying shape and size of nuclei as well as intra-nuclear objects and the positioning of the objects within the nuclear volume.

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