An open source Fiji/ImageJ plugin for 2D mouse brain sections to 3D Allen Brain Atlas registration

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Poster Session 2
Nicolas Chiaruttini (1), Bianca Ambrogina Silva (2), Olivier Burri (1), Arne Seitz (1)
1. BioImaging & Optics platform (BIOP), Faculty of Life Sciences (SV), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
2. Laboratory of Neuroepigenetics, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale Lausanne, 1015, Lausanne, Switzerland

ImageJ, Fiji, Allen Brain Atlas, 2d sections, registration, BigWarp, QuPath, elastix

Abstract text

Mapping image data to the allen brain atlas is a very common, important and often time-consuming and non trivial task in neurological research. Open source and proprietary software tools have been developed to tackle this challenge with the disadvantages of being far from a one-size-fits-all solution. 
    Each software is typically tailored for a specific use case (3D vs 3D or 2D vs 3D registration, automated / manual,  affine or free-form transformation). With the Allen Brain BIOP Aligner (ABBA), we offer a unique combination of features in the current software landscape for 2D to 3D registration: support of multiresolution images in their native file format, a convenient user interface for positioning slices along the atlas and asynchronous computation of (potentially nonlinear) registrations. This is realized by using the abstract imglib2 image library and the bigdataviewer ecosystem of Fiji, which readily provides atlas reslicing in arbitrary orientations and on-the-fly computing of image transformations. 

It takes 30 minutes for a trained user to perform a fully non-linear registration of 80 sections, including manual curation, on a ‘standard’ computer. The software contains modules to facilitate the communication with QuPath, which can be used for defining the initial data set, and for further downstream analysis after registration. The automated registration backend uses the elastix library, and manual edition of registration uses Fiji’s BigWarp plugin. Future development will include better compatibility with other software and an extensibility mechanism for adding registration methods.