Machine learning

Synonyms
Artificial intelligence

What you need to know about QuPath for fluorescence and IHC images analysis

Submitted by volker on

In the first part the workshop takes a quick tour of the different tools available in QuPath. In the second part the tools are used to analyze fluorescence and IHC images. The aim of the workshop is to help the participants getting started to use QuPath for their image analysis projects, to understands the methods applied and the results obtained and to avoid possible pitfalls.

Program

1. Project creation

2.

BIIGLE

Collection
Description

BIIGLE is a web-based software for image and video annotation that enables collaborative research on large datasets. It offers tools for manual and computer-assisted annotation, quality control and the collaboration on custom taxonomies to describe objects. BIIGLE is freely available and can be installed in cloud environments, a local network or on mobile platforms during research expeditions. The public instance on biigle.de is free for non-commercial use.

has topic
Bioimage informatics
Microscopy
Machine learning
has function
Object detection
Image annotation
Classification
BIIGLE Logo

Metric Reloaded: how to select and use your metrics

Submitted by Perrine on

The mission of Metrics Reloaded is to guide researchers in the selection of appropriate performance metrics for biomedical image analysis problems, as well as provide a comprehensive online resource for metric-related information and pitfalls. This website provides ressources such as a tool to select the best metric, as well as tutorials about the way to use and interpret metrics in image analysis.

nanoFeatures

Component
Description

MATLAB app to characterize nanoparticles imaged with super-resolution microscopy. nanoFeatures will read text and csv files from the NIKON and ONI microscopes and from the ThunderSTORM Fiji plugin, then cluster the localizations and filter by size and sphericity and finally output nanoparticle features like size, aspect ratio, and number of localizations per cluster (total and for each channel).

has topic
Bioimage informatics
Imaging
Microscopy
Super-resolution microscopy
Single molecule localization microscopy
Machine learning
Unsupervised learning
has function
Operation
Analysis
Image analysis
Image feature detection
Single molecule localisation
Object feature extraction
Shape features
Clustering
GUI first tab to browse and input files, select input type and check extra filters if needed.

ELEPHANT

Collection
Description

ELEPHANT is a platform for 3D cell tracking, based on incremental and interactive deep learning.
It implements a client-server architecture. The server is built as a web application that serves deep learning-based algorithms. The client application is implemented by extending Mastodon, providing a user interface for annotation, proofreading and visualization.

has topic
Bioimage informatics
Live sample imaging
Light-sheet microscopy
Confocal fluorescence microscopy
Machine learning
has function
Object detection
Cell tracking
Trajectory analysis
Visualisation
from https://elephant-track.github.io/#/v0.5/?id=_5-proofreading
Subscribe to Machine learning