Landmark detection LC models prediction

Description

This workflow predict landmark positions on images by using LC landmark detection models.

has topic
has function
need a thumbnail

Landmark detection LC models training

Description

This workflow trains LC landmark detection models from a dataset of annotated images.

has topic
has function
need a thumbnail

Landmark detection MSET models training

Description

This workflow trains MSET landmark detection models from a dataset of annotated images.

has function
need a thumbnail

Pixel classification for GlaS challenge with UNet

Description

This workflow segments glands from H&E stained histopathological images
from the Gland Segmentation Challenge (GlaS2015) using deep learning (UNet).
UNet implementation largely inspired from PyTorch-UNet by Milesial. 

need a thumbnail

jSLIC

Description

jSLIC superpixels - is a segmentation method for clustering similar regions - superpixels - in the given image which are usually used for other segmentation techniques. The only two parameters are average (initial) size of each superpixel and rigidity parameter in range (0,1)

has topic
has function
superpixels - ROI

VascuSynth

Description

VascuSynth is an ITK-based synthetic image generator. It synthesizes volumetric images of vascular trees and generates a .gxl file of the ground-truth tree structure. VascuSynth receives a number of .txt configuration files and is capable of generating both ground truth ('ideal') images and images with added noise. The user is capable of choosing from a set simple noise additions and artefacts.

has function

Nuclei Segmentation (CellProfiler)

Description

This workflow processes a group of images containing cells with discernible nuclei and segments the nuclei and outputs a binary mask that show where nuclei were detected. It was developed as a test workflow for Neubias BIAFLOWS Benchmarking tool.

has function

Nuclei Tracking (ImageJ)

has function
need a thumbnail

3D Fill holes (mcib3d)

Description

Runs fill holes operation on 3D images.

need a thumbnail

Maximum (3D) VIB Protocol

Description

This component convolves the image with maximum filter. Each voxel is set to the maximum value of its neighborhood. The neighborhood is defined by a kernel, which has a diameter of 3 voxels.

need a thumbnail