Image Title Category Type Description Updated
need a thumbnail MSRC Registration Toolbox Software Component

This python toolbox performs registration between 2-D microscopy images from the same tissue section or serial sections in several ways to achieve imaging mass spectrometry (IMS) experimental goals.

This code supports the following works and enables others to perform the workflows outlined in the following works, please cite them if you use this toolbox:

03/20/2019 - 13:26
need a thumbnail Nuclei Segmentation (ilastik) Software Workflow

NEUBIAS-WG5 workflow for nuclei segmentation using ilastik v1.3.2 and Python post-processing.

03/15/2019 - 15:39
Mask-RCNN Software Collection

This is an implementation of Mask R-CNN on Python 3, Keras, and TensorFlow. The model generates bounding boxes and segmentation masks for each instance of an object in the image. It's based on Feature Pyramid Network (FPN) and a ResNet101 backbone.

03/15/2019 - 12:40
need a thumbnail Nuclei Segmentation (Mask-RCNN) Software Workflow

NEUBIAS-WG5 workflow for nuclei segmentation using Mask-RCNN. The workflow uses Matterport Mask-RCNN. Keras implementation. The model was trained with Kaggle 2018 Data Science Bowl images.

03/15/2019 - 12:45
need a thumbnail Landmark detection DMBL model prediction Software Workflow

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

03/15/2019 - 03:24
need a thumbnail sumproduct Software Collection

An implementation of Belief Propagation for factor graphs, also known as the sum-product algorithm

03/15/2019 - 03:09
need a thumbnail Landmark detection DMBL model training Software Workflow

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

03/15/2019 - 03:17
need a thumbnail Landmark detection LC models prediction Software Workflow

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

03/15/2019 - 03:24
need a thumbnail Landmark detection LC models training Software Workflow

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

03/15/2019 - 02:15
need a thumbnail Landmark detection MSET models prediction Software Workflow

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

03/15/2019 - 02:03
need a thumbnail Landmark detection MSET models training Software Workflow

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

03/15/2019 - 02:04
need a thumbnail pydensecrf Software Collection

This is a (Cython-based) Python wrapper for Philipp Krähenbühl's Fully-Connected CRFs (version 2).

03/15/2019 - 01:24
PyTorch Software Collection

PyTorch is an open-source machine learning library for Python, based on Torch, used for applications such as natural language processing.

03/15/2019 - 00:52
need a thumbnail Pixel classification for GlaS challenge with UNet Software Workflow

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. 

03/15/2019 - 01:26
ContourLines Software Component

ImageJ/FIJI plugin generating contour lines with equal spacing on top of an image (using overlay).

03/14/2019 - 23:52
Atlas pyBPDL Software Collection

The Binary Pattern Dictionary Learning (BPDL) package is suitable for image analysis on a set/sequence of images to determine an atlas of a compact region. In particular, the application can be maping gene activation accross many samples, brain activations in a time domain, etc.

03/09/2019 - 09:22
BIRL: Benchmark on Image Registration methods with Landmark validation Software Collection

The project introduces a cross-platform framework for comparison of image registration methods with landmark validation (registration precision is measured by user landmarks). The project contains a set of sample images with related landmark annotations and experimental evaluation of state-of-the-art image registration methods.

Some key features of the framework:

03/09/2019 - 09:52
Logo ANHIR: Automatic Non-rigid Histological Image Registration Dataset

This dataset aims at the comparison of the automatic nonlinear image registration of 2D microscopy images of histopathology tissue samples stained with different dyes. 

03/09/2019 - 09:26
superpixels - ROI jSLIC Software Component

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)

03/08/2019 - 13:06
pyImSegm Software Collection

Collection of several basic standard image segmentation methods focusing on medical imaging. In particular, the key block/applications are (un)supervised image segmentation using superpixels, object centre detection and region growing with a shape prior. Besides the open-source code, there is also a few sample images.

 

03/08/2019 - 13:06