AI-Powered 3D Quantification

The Translucence Teravoxel Toolkit (3TK) offers unrivaled speed and flexibility, allowing the rapid generation of custom assays.

Modular and Customizable

AI-Powered 3D Quantification is the final step of our modular custom service offerings, delivering precise and robust 3D insights into the epitope of interest. If you can label it, we can quantify it.

Background

3D histological data offers significant potential but has proven challenging to quantify for much of the scientific community.

Large terabyte-scale data sets produced by tissue clearing and lightsheet imaging require extensive computational resources.

And while there are a few open source solutions for this type of quantification, their implementation often requires extensive coding experience not available to the average academic lab.

Background

The Translucence Teravoxel Toolkit (3TK) offers unrivaled speed and flexibility, allowing the rapid generation of custom assays. Integrated AI-powered classifiers allow us to generate assays with unprecedented noise rejection and the ability to separate cell types within the same fluorescence channel. 3TK software scans, detects, segments, and quantifies objects of interest across whole 3D samples, providing comprehensive insights into the epitope of interest.

Quantification of terabyte-scale datasets is enabled by cloud and cluster computing, as well as advanced memory handling and analysis routines built from the ground up which allow for scaling and rapid processing.

For brain samples, samples are warped to the Allen reference atlas.

Translucence Biosystems specializes in quantifying a wide range of epitopes and can collaborate to create custom assays for your specific epitope of interest. If you can label it, we can quantify it. 

Segmented objects can be quantified in a multitude of ways. Several metrics we can extract from segmented objects include: signal intensity, density, size, and shape.

Simply send us your stitched tiff stacks and we will send back actionable data.

AI-Powered 3D Quantification

AI-Powered 3D Quantification is the final step of our modular custom service offerings, delivering precise and robust 3D insights into the epitope of interest. If you can label it, we can quantify it.

The Translucence Teravoxel Toolkit (3TK) offers unrivaled speed and flexibility, allowing the rapid generation of custom assays. Integrated AI-powered classifiers allow us to generate assays with unprecedented noise rejection and the ability to separate cell types within the same fluorescence channel. 3TK software scans, detects, segments, and quantifies objects of interest across whole 3D samples, providing comprehensive insights into the epitope of interest.

Quantification of terabyte-scale datasets is enabled by cloud and cluster computing, as well as advanced memory handling and analysis routines built from the ground up which allow for scaling and rapid processing.

For brain samples, samples are warped to the Allen reference atlas.

Translucence Biosystems specializes in quantifying a wide range of epitopes and can collaborate to create custom assays for your specific epitope of interest. If you can label it, we can quantify it. 

Segmented objects can be quantified in a multitude of ways. Several metrics we can extract from segmented objects include: signal intensity, density, size, and shape.

Simply send us your stitched tiff stacks and we will send back actionable data.

Actionable data

Actionable data

Browse actionable insights generated by the

AI-Powered 3D Quantification

service

Browse actionable insights generated by our AI-Powered 3D Quantification services

Automated Brain-Wide Identification of Microglia with 3TK Software

The top images are a single z-plane through an intact 3D experimentally-treated brain. Iba1 immunoreactivity is shown on the left, and the corresponding cell labels from an AI-powered workflow in our 3TK software are on the right. Zoomed images show cellular morphology masks. Small seeming labels can be portions of microglia that project orthogonal to the 2D slice shown. Cell masks allow for counts, shape analysis, and fluorescence intensity measurements.

β-Amyloid Plaque Staining and Labels in a 5xFAD Alzheimer’s Model Mouse Brain

Single z-planes through a 5xFAD mouse brain demonstrate the brain-wide pattern of β-amyloid aggregates. On the left is immunoreactivity measured with an anti-β-amyloid antibody. On the right, an AI-powered workflow in our 3TK software identifies and labels plaques throughout the brain.

Machine Learning-Enabled Microglia Shape and Count Workflows

We trained machine learning algorithms to help segment individual microglia. In one case, we predicted the full volume of microglia to make shape determinations and in the other case we identified only the soma to generate counts.

Brain-Wide Quantification of Plaque-Associated Microglia

In 5xFAD mice, Iba1(+) microglia colocalize with Amyloid plaques and become activated, retracting processes and taking on a distinct shape not seen in WT mouse brains. We trained our Al-powered workflows to selectively detect these activated plaque-associated microglia (PAMs) and not the majority of the Iba1(+) microglia in the brain that are in a homeostatic state. The PAM levels in Cerebellum, Visual and Somatomotor Areas are consistent with the Amyloid levels detected in the same mice. Across hundreds of brain area, the data from our Amyloid and PAM whole-brain quantification workflows are strongly correlated.

AI-powered Separation of Two Populations of Objects in the Same Fluorescence Channel

Clearing and staining of a whole brain from a 5xFAD Alzheimer’s Disease model mouse with an antibody recognizing β-Amyloid.

AI-powered tools determine the probability that an object is a plaque (red) or cell (green). Our 3TK workflows can then perform brain-wide regional quantification of independent object populations extracted from the same fluorescence channel.

3TK-mediated Quantification of Npas4 After Light Exposure

Our Translucence Teravoxel ToolKit (3TK) software uses AI-powered workflows to identify individual Npas4(+) neurons throughout the cleared and stained intact mouse brain.

Each brain is computationally warped to the Allen Reference Brain and neurons are registered to an anatomical map to determine Npas4 expression metrics across 100’s of brain regions.

We have collapsed the hierarchical annotations into larger regions to demonstrate brain-wide Npas4 expression levels in 14 brains from mice exposed to light for various durations after housing in the dark for 24h.

Brain-Wide Quantification of Neuronal Activity in 100’s of Brain Regions

These 2D heatmaps are drawn from 3D whole-brain data sets and show the level of Npas4 expression determined from the Npas4 staining intensity of individual neurons.

The Npas4 signal is quantified in 100’s of brain regions over time. We have plotted data from a few exemplar regions in the bottom left.

The volcano plot shows brain regions in blue with statistically significant elevations of Npas4 expression after light exposure.

Brain-Wide Regional Quantification of β-Amyloid Plaques

After segmenting amyloid plaques throughout the brain, we register individual brains with the Allen Reference Brain, using the warping function to shift the x,y,z coordinated of individual plaques into a standard coordinate space. We then use the 3D brain map to produce automated regional quantification of amyloid plaque density.

Interested in AI-Powered 3D Quantification?

AI-Powered 3D Quantification delivers precise and robust 3D insights into the epitope of interest. If you can label it, we can quantify it.

NIH-funded tissue clearing kit users are eligible for a discounted rate on quantification services to assist in your sample analysis.

When you contact us about AI-Powered 3D Quantification services, please indicate in the comments section that you are using our kit and provide us with the email that you purchased the kit(s) with.

Heading

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Suspendisse varius enim in eros elementum tristique. Duis cursus, mi quis viverra ornare, eros dolor interdum nulla, ut commodo diam libero vitae erat. Aenean faucibus nibh et justo cursus id rutrum lorem imperdiet. Nunc ut sem vitae risus tristique posuere.

Heading 1

Heading 2

Heading 3

Heading 4

Heading 5
Heading 6

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur.

Block quote

Ordered list

  1. Item 1
  2. Item 2
  3. Item 3

Unordered list

  • Item A
  • Item B
  • Item C

Text link

Bold text

Emphasis

Superscript

Subscript

Heading 1

Heading 2

Heading 3

Heading 4

Heading 5
Heading 6

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur.

Block quote

Ordered list

  1. Item 1
  2. Item 2
  3. Item 3

Unordered list

  • Item A
  • Item B
  • Item C

Text link

Bold text

Emphasis

Superscript

Subscript

Heading 1

Heading 2

Heading 3

Heading 4

Heading 5
Heading 6

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur.

Block quote

Ordered list

  1. Item 1
  2. Item 2
  3. Item 3

Unordered list

  • Item A
  • Item B
  • Item C

Text link

Bold text

Emphasis

Superscript

Subscript

Heading 1

Heading 2

Heading 3

Heading 4

Heading 5
Heading 6

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur.

Block quote

Ordered list

  1. Item 1
  2. Item 2
  3. Item 3

Unordered list

  • Item A
  • Item B
  • Item C

Text link

Bold text

Emphasis

Superscript

Subscript

Heading 1

Heading 2

Heading 3

Heading 4

Heading 5
Heading 6

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur.

Block quote

Ordered list

  1. Item 1
  2. Item 2
  3. Item 3

Unordered list

  • Item A
  • Item B
  • Item C

Text link

Bold text

Emphasis

Superscript

Subscript

Request a quote

Please select which services are you interested in we will reach out to you shortly

Custom services

Contact information

Back
Next

Thank you!

Your submission has been received

Something went wrong while submitting the form.
Please, contact us via email info@translucencebio.com