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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.


Provides a method for exposing gene expression patterns from different larval brains in a common reference space. Larvalign is an open source computational framework that mainly focuses on allowing the registration of microscope images of the central nervous system (CNS) of the third instar Drosophila larva. It includes functionalities for image processing and quality assessment. The software can be applied for help generate a curated database of registered expression patterns.

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.

Amira 3D Software for Life Sciences

Allows users to visualize, manipulate, and understand data from imaging modalities such as computed tomography, microscopy or Magnetic resonance imaging (MRI). Amira 3D Software for Life Sciences provides features to import and process 2D and 3D images data, visualization techniques and tools for visual analysis. Users can also create and share presentations. The base product can be customized by adding functional extensions to fit special needs in different application areas.