Provides a cleared 3D brain image processing and analysis methods for light-sheet fluorescence microscopy (LSFM). CUBIC is a standalone software getting its name from the CUBIC protocol wich is a chemical sample clearing protocol especially designed for brain tissues. It provides multiple functionalities: (i) The image file conversion and manipulation, (ii) the detection of sample edges, (iii) the brain alignent and (iv) the atlasing of the brain sample.
An automated workflow for processing large multiview, multi-channel, multi-illumination time-lapse selective plane illumination microscopy (SPIM) data on a single workstation or in parallel on a HPC cluster. The pipeline relies on snakemake to resolve dependencies among consecutive processing steps and can be easily adapted to any cluster environment for processing SPIM data in a fraction of the time required to collect it.
A FIJI plugin for fusing bi-directionally recorded microscopic image volumes. BiDiFuse merges image stacks via 3D rigid transformations. The method is broadly applicable, considering its compatibility with all optical sectioning microscopes and does not rely on fiducial markers for image registration.
Allows automatic 3D stitching of teravoxel-sized tiled images. TeraStitcher was initially developed for stitching images generated by the confocal laser scanning microscopy (CLSM) microscope. The software specifies the requirements of the stitching problem when teravoxel-sized images are involved, and then use the system resources to perform the stitching of these images. It is available both as standalone application and as plugin of the free software Vaa3D.
Enables high speed three-dimensional imaging of large samples at high resolution. VIsoR can achieve image acquisition of an entire mouse brain in a couple of hours with individual synaptic spines in cortical neurons visible. This method can be applied for the study of 3D structures of other biological and pathological specimen beyond brain mapping.
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