Localizing microemboli within the rodent brain through block-face imaging and atlas registration

AbstractWe describe our connectomics pipeline for processing tracer injection data for the brain of the common marmoset (Callithrix jacchus). Brain sections were imaged using a batch slide scanner (NanoZoomer 2.0-HT) and we used artificial intelligence to precisely segment the anterograde tracer signal from the background in the fluorescence images. The shape of each brain was reconstructed by reference to a block-face and all data was mapped into a common 3D brain space with atlas and 2D cortical flat map. To overcome the effect of using a single template atlas to specify cortical boundaries, each brain was cytoarchitectonically annotated and used for making an individual 3D atlas. Registration between the individual and common brain cortical boundaries in the flat map space was done to absorb the variation of each brain and precisely map all tracer injection data into one cortical brain space. We describe the methodology of our pipeline and analyze tracer segmentation and brain registration accuracy. Results show our pipeline can successfully process and normalize tracer injection experiments into a common space, making it suitable for large-scale connectomics studies with a focus on the cerebral cortex.

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Effects of Vibration on the Preparation of Ultrathin Sections

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010007223x ◽

1973 ◽

Vol 31 ◽

pp. 358-359

Author(s):

Joseph M. Blum ◽

Edward P. Gargiulo ◽

J. R. Sawers

Keyword(s):

Cutting Speed ◽

Ground Level ◽

Environmental Vibration ◽

Block Face ◽

Ultrathin Sections ◽

Embedding Medium ◽

Thickness Variations ◽

Building Walls ◽

Cutting Direction ◽

Diamond Knife

It is now well-known that chatter (Figure 1) is caused by vibration between the microtome arm and the diamond knife. It is usually observed as a cyclical variation in “optical” density of an electron micrograph due to sample thickness variations perpendicular to the cutting direction. This vibration might be induced by using too large a block face, too large a clearance angle, excessive cutting speed, non-uniform embedding medium or microtome vibration. Another prominent cause is environmental vibration caused by inadequate building construction. Microtomes should be installed on firm, solid floors. The best floors are thick, ground-level concrete pads poured over a sand bed and isolated from the building walls. Even when these precautions are followed, we recommend an additional isolation pad placed on the top of a sturdy table.

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Faculty Opinions recommendation of Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1022557.793507804 ◽

2015 ◽

Author(s):

Alpha Yap

Keyword(s):

Electron Microscopy ◽

Scanning Electron Microscopy ◽

Three Dimensional ◽

Face Scanning ◽

Block Face ◽

Scanning Electron

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Faculty Opinions recommendation of Expression, activity and regulation of CYP3A in human and rodent brain.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1120909.577176 ◽

2008 ◽

Author(s):

Pierre Baumann

Keyword(s):

Rodent Brain ◽

Expression Activity

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Progress of In Vivo Electroporation in the Rodent Brain

Current Gene Therapy ◽

10.2174/1566523214666140424145305 ◽

2014 ◽

Vol 14 (3) ◽

pp. 211-217 ◽

Cited By ~ 2

Author(s):

Xue-Feng Ding ◽

De-Lin Ma ◽

Qiang Zhang ◽

Wei Peng ◽

Ming Fan ◽

...

Keyword(s):

In Vivo Electroporation ◽

Rodent Brain

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The Model for Calculating Elastic Modulus and Poisson's Ratio of Coal Body

The Open Fuels & Energy Science Journal ◽

10.2174/1876973x20131011004 ◽

2013 ◽

Vol 6 (1) ◽

pp. 36-43 ◽

Cited By ~ 3

Author(s):

Ai Chi ◽

Li Yuwei

Keyword(s):

Elastic Modulus ◽

Poisson’S Ratio ◽

Fractured Rock ◽

Rock Block ◽

Poisson's Ratio ◽

Linear Elastic ◽

Study Results ◽

The Face ◽

Block Face ◽

Coal Rock

Coal body is a type of fractured rock mass in which lots of cleat fractures developed. Its mechanical properties vary with the parametric variation of coal rock block, face cleat and butt cleat. Based on the linear elastic theory and displacement equivalent principle and simplifying the face cleat and butt cleat as multi-bank penetrating and intermittent cracks, the model was established to calculate the elastic modulus and Poisson's ratio of coal body combined with cleat. By analyzing the model, it also obtained the influence of the parameter variation of coal rock block, face cleat and butt cleat on the elastic modulus and Poisson's ratio of the coal body. Study results showed that the connectivity rate of butt cleat and the distance between face cleats had a weak influence on elastic modulus of coal body. When the inclination of face cleat was 90°, the elastic modulus of coal body reached the maximal value and it equaled to the elastic modulus of coal rock block. When the inclination of face cleat was 0°, the elastic modulus of coal body was exclusively dependent on the elastic modulus of coal rock block, the normal stiffness of face cleat and the distance between them. When the distance between butt cleats or the connectivity rate of butt cleat was fixed, the Poisson's ratio of the coal body initially increased and then decreased with increasing of the face cleat inclination.

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