"The true mystery of the world is in visible, not in invisible"
-- Oscar Wilde
The reason this site was created
Brain Imaging Informatics is dedicated to design of automatic image analysis and visualization technologies for human brain cytoarchitecture. It means processing of brain images at microscopic resolution (1 micron or better). Recent progress in imaging technologies, including MRI and fMRI
Neuronal clustering map with isotropic structuring element
As the first step of this study we developed the algorithm of detection of neuronal clusters using the approach known in Mathematical Morphology as “distance map”. The notion of the morphological distance map is based on metric defined by erosion
“Qute Brain Browser” – 3D multi-modal voxel-based image viewer
Why BigBrain data set is so important for cytoarchitectonic studies? The BigBrain model itself, among other goals (please, use this link for more information: BigBrain Project) was developed to be used as a publicly-available source of microscopical human brain data at
The story of MCG: lost opportunity.
This story is a sad example of how illiterate bureaucracy, for quite poorly specified reason, is capable to stop a pioneering research and delayed by many years the opportunity for the progress in an important area of science. 1. The
A “Tale of Two Cities” – new version, neuroscience – style.
Peer review: “Katrin Amunts, Vadim Istomin, Axel Schleicher, Karl Zilles. Postnatal development of the human primary motor cortex: a quantitative cytoarchitectonic analysis” Anat. Embryol., (1995) 192:557-571. and “K. Amunts, A. Schleicher, K.Zilles. Persistence of layer 4 in the primary motor
Nissl-stained sections segmentation using algorithms of Mathematical Morphology
The main part of presented algorithm is sequential homotopic thinning transformation, “invented” by a group of mathematicians, including F. Meyer (1976), Ch. Lantuejoul (1978), and headed by J.Serra, from Center for Mathematical Morphology, Fontainebleau, France. Many transformations based on thinning
Comparison of anisotropic distance maps for areas 10m and 37.
High-resolution Nissl-stained sections of human brain were downloaded from Allen Brain Atlases portal using published API. Image resolution was 1 micrometer or better. Depending upon the section region, total size of JPEG files varied from 300MB to 1.5 GB. Between
“Rich-club” member candidates areas form a distinct group
Based on preliminary results of regression analysis, it seems possible to conclude that our initial hypothesis (here) was true: rich-club members areas differ from non-members by different topology of clusterization pattern. Cluster population regression data show that “rich-club” member candidates
Semantic segmentation of human brain cortex with UNET-like architecture using SONY Neural Network Console
Here we present better segmentation result using a modification of the UNET network published in version 1.5 of SONY Neural Network Console. Training images are prepared using the algorithm described here. Images were visually inspected and corrected, where necessary, using