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Analyzes, processes and visualizes multi-dimensional microscopy images. BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes.

RAMTaB / Robust Alignment of Multi-Tag Bioimages

Permits to align images in a multi-tag fluorescence image stack. RAMTaB is a block-based registration method that can select a reference image with maximal overlap. It is able to determine sub-pixel shifts between phase contrast images in a multi-tag fluorescence image stack. The tool is not sensible to brightness and contrast variations. It has difficulties with poor quality phase contrast images containing blur due to the changes in the plane at which camera sets its focus while taking the images.

Register Virtual Stack Slices

Provides a method for elastic and consistent registration of histological sections. Register Virtual Stack Slices is an ImageJ plugin that uses a sequence of image slices stored in a folder, and offers a list of registered image slices (with enlarged canvas). It can perform six types of image registration techniques: (i) translation, (ii) rigid (translation + rotation), (iii) similarity (translation + rotation + isotropic scaling), (iv) affine, (v) elastic and (vi) moving least squares.