Publications by authors named "Alexander S Tolpygo"

4 Publications

  • Page 1 of 1

An active texture-based digital atlas enables automated mapping of structures and markers across brains.

Nat Methods 2019 04 11;16(4):341-350. Epub 2019 Mar 11.

Department of Physics, University of California, San Diego, CA, USA.

Brain atlases enable the mapping of labeled cells and projections from different brains onto a standard coordinate system. We address two issues in the construction and use of atlases. First, expert neuroanatomists ascertain the fine-scale pattern of brain tissue, the 'texture' formed by cellular organization, to define cytoarchitectural borders. We automate the processes of localizing landmark structures and alignment of brains to a reference atlas using machine learning and training data derived from expert annotations. Second, we construct an atlas that is active; that is, augmented with each use. We show that the alignment of new brains to a reference atlas can continuously refine the coordinate system and associated variance. We apply this approach to the adult murine brainstem and achieve a precise alignment of projections in cytoarchitecturally ill-defined regions across brains from different animals.
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http://dx.doi.org/10.1038/s41592-019-0328-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6736610PMC
April 2019

A high-throughput neurohistological pipeline for brain-wide mesoscale connectivity mapping of the common marmoset.

Elife 2019 02 5;8. Epub 2019 Feb 5.

Laboratory for Marmoset Neural Architecture, RIKEN Center for Brain Science, Wako, Japan.

Understanding the connectivity architecture of entire vertebrate brains is a fundamental but difficult task. Here we present an integrated neuro-histological pipeline as well as a grid-based tracer injection strategy for systematic mesoscale connectivity mapping in the common marmoset (). Individual brains are sectioned into ~1700 20 µm sections using the tape transfer technique, permitting high quality 3D reconstruction of a series of histochemical stains (Nissl, myelin) interleaved with tracer labeled sections. Systematic in-vivo MRI of the individual animals facilitates injection placement into reference-atlas defined anatomical compartments. Further, by combining the resulting 3D volumes, containing informative cytoarchitectonic markers, with in-vivo and ex-vivo MRI, and using an integrated computational pipeline, we are able to accurately map individual brains into a common reference atlas despite the significant individual variation. This approach will facilitate the systematic assembly of a mesoscale connectivity matrix together with unprecedented 3D reconstructions of brain-wide projection patterns in a primate brain.
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http://dx.doi.org/10.7554/eLife.40042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6384052PMC
February 2019

High-Throughput Method of Whole-Brain Sectioning, Using the Tape-Transfer Technique.

PLoS One 2015 16;10(7):e0102363. Epub 2015 Jul 16.

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America.

Cryostat sectioning is a popular but labor-intensive method for preparing histological brain sections. We have developed a modification of the commercially available CryoJane tape collection method that significantly improves the ease of collection and the final quality of the tissue sections. The key modification involves an array of UVLEDs to achieve uniform polymerization of the glass slide and robust adhesion between the section and slide. This report presents system components and detailed procedural steps, and provides examples of end results; that is, 20 μm mouse brain sections that have been successfully processed for routine Nissl, myelin staining, DAB histochemistry, and fluorescence. The method is also suitable for larger brains, such as rat and monkey.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0102363PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4504703PMC
April 2016

A low-cost technique to cryo-protect and freeze rodent brains, precisely aligned to stereotaxic coordinates for whole-brain cryosectioning.

J Neurosci Methods 2013 Sep 29;218(2):206-13. Epub 2013 Mar 29.

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.

A major challenge in the histological sectioning of brain tissue is achieving accurate alignment in the standard coronal, horizontal, or sagittal planes. Correct alignment is desirable for ease of subsequent analysis and is a prerequisite for computational registration and algorithm-based quantification of experimental data. We have developed a simple and low-cost technique for whole-brain cryosectioning of rodent brains that reliably results in a precise alignment of stereotactic coordinates. The system utilises a 3-D printed model of a mouse brain to create a tailored cavity that is used to align and support the brain during freezing. The alignment of the frozen block is achieved in relation to the fixed edge of the mold. The system also allows for two brains to be frozen and sectioned simultaneously. System components, procedural steps, and examples of the end results are presented.
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http://dx.doi.org/10.1016/j.jneumeth.2013.03.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4265468PMC
September 2013