Component

A Component is an implementation of certain image processing / analysis algorithms.

Each component alone does not solve a Bioimage Analysis problem.

These problems can be addressed by combining such components into workflows.

Description

It stitches 3D tiles from terabyte-size microscopy datasets. Stitching does not require any prior information on the actual positions of the tiles, sample fiducials, or conversion of raw TIFF images, and the stitched images can be explored instantly.

MosaicExplorerJ was specifically designed to process lightsheet microscopy datasets from optically cleared samples. It can handle multiple fluorescence channels, dual-side lightsheet illumination and dual-side camera detection.

Description

 This ImageJ function automatically or interactively sets lower and upper threshold values, segmenting grayscale images into features of interest and background.

has function
need a thumbnail
Description

FluoGAN is a fluorescence image deconvolution software combining the knowledge of acquisition physical model with gan. It takes a fluctuating sequence of blurred, undersampled and noisy images of the sample of interest  fixed sample as input from wide field or confocal and returns a super resolved image.

FluoGan
Description

Orthanc aims at providing a simple, yet powerful standalone DICOM server. It is designed to improve the DICOM flows in hospitals and to support research about the automated analysis of medical images. Orthanc lets its users focus on the content of the DICOM files, hiding the complexity of the DICOM format and of the DICOM protocol.

Orthanc can turn any computer running Windows, Linux or OS X into a DICOM store (in other words, a mini-PACS system). Its architecture is lightweight and standalone, meaning that no complex database administration is required, nor the installation of third-party dependencies.

What makes Orthanc unique is the fact that it provides a RESTful API. Thanks to this major feature, it is possible to drive Orthanc from any computer language. The DICOM tags of the stored medical images can be downloaded in the JSON file format. Furthermore, standard PNG images can be generated on-the-fly from the DICOM instances by Orthanc.

Orthanc also features a plugin mechanism to add new modules that extends the core capabilities of its REST API. A Web viewer, a PostgreSQL database back-end, a MySQL database back-end, and a reference implementation of DICOMweb are currently freely available as plugins.

orthanc
Description

Correlia is an open-source ImageJ/FIJI plug-in for the registration of 2D multi-modal microscopy data-sets. The software is developed at ProVIS - Centre for Correlative Microscopy and is specifically designed for the needs of chemical microscopy involving various micrographs as well as chemical maps at different resolutions and field-of-views.

Correlia