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

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
Description

The empanada-napari plugin is built to democratize deep learning image segmentation for researchers in electron microscopy (EM). It ships with MitoNet, a generalist model for the instance segmentation of mitochondria. There are also tools to quickly build and annotate training datasets, train generic panoptic segmentation models, finetune existing models, and scalably run inference on 2D or 3D data. To make segmentation model training faster and more robust, CEM pre-trained weights are used by default. These weights were trained using an unsupervised learning algorithm on over 1.5 million EM images from hundreds of unique EM datasets making them remarkably general.

Empanada-napari
Description

Removal of heterogeneous background from image data of single-molecule localization microscopy, using extreme value-based emitter recovery (EVER).

Quote:

EVER requires no manual adjustment of parameters and has been implemented as an easy-to-use ImageJ plugin that can immediately enhance the quality of reconstructed super-resolution images. This method is validated as an efficient way for robust nanoscale imaging of samples with heterogeneous background fluorescence, such as thicker tissue and cells.

has function
Description

The napari-pyclesperanto-assistant is a yet experimental napari plugin for building GPU-accelerated image processing workflows targeting life-sciences and bio-image analysis. It is part of the clEsperanto project. It uses pyclesperanto and pyopencl as backend for processing images.

has function
Description

AnnotatorJ is a Fiji Plugin to ease annotation of images, particulrly useful for Deep Learning or to validate an alogorithm. Interestingly, it allows annotation for instance segmentation, semantic segmentation, or bounding box annotations. It includes toolssuch as active contours to ease these annotations.

has topic
has function
annotatorJ