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 of human brain, increased the demand for precise anatomical localization of specific areas of brain activity. As a result, mapping of cytoarchitectonic areas of human brain cortex experiences nowadays true revolution, in both technological and scientific domains. Therefore, the main focus of our discussions will be processing, analysis and visualization of the cytoarchitecture of neocortex, with possible digressions into historic, software engineering and even ethical issues.

A few years ago we had a chance to provide our small contribution to BigBrain project(BigBrain-2015, BigBrain-2017). Initially the idea of this project looked quite remarkable: it was introduced as a first attempt in the history of the Neuroscience to build three-dimensional map of the entire human brain at  microscopic resolution.  As a part of gigantic billion-dollar funded European Human Brain Project, BigBrain project is headed by the Institute for Neuroscience and Medicine (INM-1), Juelich, Germany.  All relevant information can be found using this link:

Initially this site was created as a tool for information exchange between participants of BigBrain projects. However, for whatever reason, our attempt to influence its direction clearly outplayed the will of the management to accept it. Moreover, during the past year it became quite clear that BigBrain project, similarly to the whole Human Brain Project, is failing to live up to its promise.

The problem is: maximal resolution of image data shared by BigBrain project site is 20 microns.  As it becomes obvious to anyone familiar with the microscope, 20-microns resolution is NOT A MICROSCOPIC resolution. It is better than MRI, but  does not reveal neurons.

One micron-resolution images ARE AVAILABLE, but the management of the BigBrain project choose not to share them, even though it is technically quite possible. As a result, this unique data set of uninterrupted sequence of 7000+ sections through the whole brain cannot be used for CYTOARCHITECTONIC studies at neuronal level. To show some possibilities of modern image processing technologies at microscopic resolution for cytoarchitectonic studies I decided to publish these pages as WordPress site.

The second problem is visualization of microscopic brain structure in 3D. Again, publicly available viewers (as, for example, JuBrain or Big Brain interactive atlas viewer) show high-resolution images only in 2D. Three-dimensional reconstruction fails to reach 1 micron resolution. Thus, the second topic of this site is dedicated to demonstration of possible solutions of this problem (“Qute Brain browser“).

So, if you are interested in development of new algorithms for analysis or mapping of the cytoarchitectonic features of human brain cortex, please, check these articles:

How reliably Grey Level Index technology (K. Zilles, A.Schleicher, K.Amunts) can be used for cortical mapping?

Why BigBrain data set needs better image viewer?

How to use Watersheds algorithm for reliable segmentation of cortical neurons?

You might also check this page, where the list of useful resources is maintained.

However, we must offer our apologies to a “chance reader” for missing links, empty pages and some apparent lack of coherence between different topics. Please, understand, these pages reflect ongoing development of a complicated technology rather ambitiously implemented with very limited resources, let alone – clear lack of funding. Hopefully, with time the content will improve and missing paragraphs, pages and links will gradually disappear.

Also, please feel free to leave your comments, as long as their are substantial, objective and motivated by professional interests. We will do our best to respond ASAP.

My professional profile is here: profile. Additionally, if you would like to see some demos of our results and applications, please, use this link:

Thank you!

Vadim V. Istomin, MD, PhD

New York

Copyright © 2017-2019, Brain Imaging Informatics, LLC

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