A collection is a software that encapsulate a set of bioimage components and/or workflows.

SPHIRE

Description

SPHIRE is a new software suite designed for easy access to cryo electron microscopy with the clear goal of quality assessment and result reproducibility by statistical resampling. While being well suited for cryo-EM novices, experienced users will find comfort in the accessibility of almost every possible variable in advanced option tabs and the transparent, easily customizable Python-based framework for non-standard processing pipelines. In a visually appealing and easy-to-use graphical user interface (GUI) the user will find an array of programs which will guide through the complete process of high-resolution cryo-EM. This begins with movie frame alignments (movie), CTF estimation of raw electron micrographs (cter) and picking/stack creation (window) and continues with reproducible 2-D classification (isac), reproducible initial model generation (viper), automatic gold-standard 3-D refinement (meridien), local resolution estimation and filtering (localres), up to the 3-D sorting of different conformational states based on the statistical 3-D variability of the data (sort3D).

need a thumbnail

ImageM

Description

ImageM integrates into a GUI several algorithms for interactive image processing and analysis. Interface is largely inspired from the open source software "ImageJ".

need a thumbnail

BioImage Model Zoo

Description

This is a database of pretrained deep Learning models. 

has topic
need a thumbnail

LobSTer

Description

LobSTEr : handle terabyte of data without concerns about the memory available .

75 workflows available 

no programming , matlab based 

need a thumbnail

IR tools

Description

A MATLAB Package of Iterative Regularization Methods and Test Problems for Linear Inverse Problems (for Matlab Version 9.3 or later).

need a thumbnail

MorphoNet

Description

MorphoNet is a novel concept of web-based morphodynamic browser to visualise and interact with complex datasets, with applications in research and teaching. 

MorphoNet offers a comprehensive palette of interactions to explore the structure, dynamics and variability of biological shapes and its connection to genetic expressions. 

By handling a broad range of natural or simulated morphological data, it fills a gap which has until now limited the quantitative understanding of morphodynamics and its genetic underpinnings by contributing to the creation of ever-growing morphological atlases.

pyimagej

Description

pyimagej provides a set of wrapper functions for integration between ImageJ and Python.

It also provides a high-level entry point for invoking ImageJ server APIs.

need a thumbnail

PSFj

Description

PSFj is a software tool that automatically analyses the full field-of-view (FOV) performance of a given fluorescence microscope/objective lens combination with respect to its optical resolution and chromatic aberrations. PSFj provides reporting functions to document the momentary performance of a system and it allows for the export of the obtained data, e.g. for image restoration purposes. PSFj is based on ImageJ and JAVA, and runs on Windows, Mac, and Linux PCs as a stand-alone application.

has topic
need a thumbnail

NucleusJ

Description

Quote

Starting from image stacks, the nuclear boundary as well as nuclear bodies are segmented. As output, NucleusJ automatically measures 15 parameters quantifying shape and size of nuclei as well as intra-nuclear objects and the positioning of the objects within the nuclear volume.

has function