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.
Reconstructs and makes complex datasets easily accessible. BigStitcher is an ImageJ plugin that enables interactive visualization, precise alignment, real-time fusion, deconvolution, support for alignment of multi-tile acquisition taken from different physical orientations, or so-called multi-tile views. It can also be used for doubling the size of specimens that can be imaged, while further orthogonal views can render the resolution isotropic.
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.
Assists in focusing microscopic images of 3D objects and organisms. Extended Depth of Field is based on different wavelet algorithms. This ImageJ plugin offers users two interfaces: a simplified mode and an expert mode with a complete set of parameters. It benefits from a RGB to grayscale conversion method that assures contrast and intensity in order to process color data.
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