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Study Design


Our Approach


Overview of imaging, study design and analysis 

Imaging and full resolution data

We use TissueCyte™ serial two-photon tomography microscopes to generate 3D visualizations of whole tissue specimens. These automated imaging systems integrate serial sectioning with 2-photon multichannel imaging to acquire full volumetric datasets. These systems are capable of generating high quality standardized datasets as demonstrated in their use by The Allen Institute for Brain Science for their Allen Mouse Brain Connectivity Atlas. Watch the video below for details of the project and demonstration of the TissueCyte™ Systems.

We excel in creating whole brain reconstructions in small model systems such as mice and rats. As demonstrated above, whole brains are imaged by STP Tomography on our TissueCyte™ platform and result in whole brain images with flexible coronal or sagittal spacing with submicron in-plane resolution. This technology allows us to image the entire intact tissue sample, while retaining the native tissue integrity, thus creating rich fully aligned 3D datasets. Left is a full resolution example dataset demonstrating a whole brain sampled at 1.2 micron in plane (XY) and 100 micron coronal spacing (Z).

GFP targeted AAV infection of Mouse Brain.

(Green: GFP, Red: autofluorescence) .

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Standard Imaging Deliverables

What you will receive:

  • Full resolution 3 color channel Tiffs

  • Full Study Summary report

TissueCyte single channel mouse brain
Ch1 (Red)
TissueCyte single channel mouse brain
Ch3 (Blue)
TissueCyte single channel mouse brain
Ch2 (Green)
TissueCyte multi-channel mouse brain
Composite (RGB)

Study Design

At TissueVision, we work closely with all of our clients to help them make the new discoveries they are after. We know that developing a new assay can create its own unique set of challenges, and we are here to help you navigate the critical decisions that will make your experiment a success.


Our high-throughput imaging services allow the capacity to perform studies involving tens to hundreds of samples that deliver results with high statistical power and biomedical relevance. In addition to our atlasing services, we also offer full analysis packages. For instance, we can perform segmentation and quantification of the regional density distributions of your target of interest. This can be a valuable service for comparative analysis across cohorts of animal models. From these services you will receive a detailed report profiling the regional density distributions of your target from the brain regions of your choice for all samples in your study.


In addition to our standard brain analysis services, we are open to developing novel analysis assays targeted to your tissue of interest. Please contact us for information.

Registered mouse brain to Allen Mouse Common Coordinte Framework v3.0.
Registered mouse brain to Allen Mouse Common Coordinte Framework v3.0
Registered mouse brain to Allen Mouse Common Coordinte Framework v3.0

For mouse brain datasets acquired through all of our Brain Imaging services, we offer our Brain Atlasing. Through this service, we will register each of your brain samples to a standard reference atlas to provide a map for regional analysis of your samples.

Currently we offer registration to the Allen Mouse Brain Reference Atlas, © 2004 Allen Institute for Brain Science, using the Allen Mouse Common Coordinate Framework v3.0 described in the Allen Mouse Brain Connectivity Atlas © 2011 Allen Institute for Brain Science (Oh, S.W. et al. 2014; A mesoscale connectome of the mouse brain, Nature 508: 207-214. doi:10.1038/nature13186). We can offer complete regional analysis or if you are interested in key brain regions, we can provide hemispheric maps as well as targeted mapping.

From this service you will receive a direct mapping of the atlas regions of your choice registered to the downsampled version of your dataset. In addition, you will receive an ontology key to identify the brain regions from the annotated atlas. If you are interested in other atlases, we have the capacity to reference your data to many standard reference atlases, please contact us for more information.

Study Design
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