Image Title Category Type Description Updated
need a thumbnail Filament Tracing LocThresh (ImageJ) Software Workflow

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,

01/23/2020 - 17:33
need a thumbnail Filament Tracing Tubeness (ImageJ) Software Workflow

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.

01/23/2020 - 17:29
need a thumbnail Neuron Tracing Vaa3D (MOST) Software Workflow

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

01/23/2020 - 17:21
need a thumbnail Neuron Tracing Vaa3D (MST) Software Workflow

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

01/23/2020 - 17:16
need a thumbnail Neuron Tracing 3D (Rivuletpy) Software Workflow

Rivuletpy dockerised workflow for BIAFLOWS.

01/23/2020 - 17:11
need a thumbnail Neuron Tracing Vaa3D (App2) Software Workflow

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

01/23/2020 - 16:39
need a thumbnail Object Tracking (MU-Lux-CZ) Software Workflow

Cell tracking using MU-Lux algorithm.

01/23/2020 - 16:34
need a thumbnail Object Tracking (Octave) Software Workflow

Nuclei tracking in 2D time-lapse with Octave tracker (adapted from Matlab LOBSTER version.

01/23/2020 - 16:19
need a thumbnail Object Tracking (ImageJ) Software Workflow

Object tracking. For each time-frame, an image mask is obtained from median filtering (user defined radius), thresholding (user defined level) and hole filling. Convex objects are split apart by distance map watershed from regional intensity maxima (user defined noise tolerance), eroded (user defined radius) and analyzed as 3D particles (assuming some overlap between objects from a frame to the next frame). Finally, division events are analyzed and accounted for to relabel objects.

01/23/2020 - 16:13
need a thumbnail pyimagej Software Collection

pyimagej provides a set of wrapper functions for integration between ImageJ and Python.

It also provides a high-level entry point for invoking ImageJ server APIs.

01/23/2020 - 16:08
need a thumbnail Nuclei Tracking (TrackMate) Software Workflow

Track non-dividing particles in 2D time-lapse image.

01/23/2020 - 16:09
need a thumbnail Particle Tracking (ImageJ) Software Workflow

Particle tracking in 2D time-lapse based on linking closest regional intensity minima (user defined noise tolerance) detected from Laplacian of Gaussian filtered images (user defined radius). A maximum linking distance is set (user defined).

01/23/2020 - 16:00
need a thumbnail Nuclei Segmentation 3D (Ilastik) Software Workflow

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

01/23/2020 - 15:54
need a thumbnail Nuclei Segmentation 3D watershed (ImageJ) Software Workflow

The macro will segment nuclei and separate clustered nuclei in a 3D image using a 2D Gaussian blur, followed by Thresholding, 2D hole filling and a 2D watershed. As a result an index-mask image is written for each input image.

01/23/2020 - 15:39
need a thumbnail Nuclei Segmentation (U-Net) Software Workflow

U-Net segmentation as presented in Reference Publication. The model predicts three classes: background, edge and foreground. The model was trained with Kaggle Data Science Bowl (DSB) 2018 training set.

01/23/2020 - 15:16
need a thumbnail Nuclei Segmentation (DeepCell) Software Component

Nuclei Segmentation using Deep Learning for single cell analysis (DeepCell).

01/23/2020 - 14:48
need a thumbnail FeatureJ Hessian Software Component

This plugin computes for each image element (pixel/voxel) the eigenvalues of the Hessian, which can be used for example to discriminate locally between plate-like, line-like, and blob-like image structures

01/23/2020 - 14:05
need a thumbnail Spot Detection 3D Hessian (ImageJ) Software Workflow

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

01/23/2020 - 14:11
need a thumbnail Spot Detection 3D (Icy) Software Workflow

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

01/23/2020 - 13:52
need a thumbnail Spot Detection Dmap (ImageJ) Software Workflow

This workflow detects spots in a 2D image by filtering the image by Laplacian of Gaussian (user defined radius), thresholding (user defined threshold) and finding local intensity maxima in mask distance map (Dmap).

01/23/2020 - 13:35