Neuroinflammatory Diseases

Brain-wide measurements of neuroinflammatory responses within the CNS via the microglial marker Iba1.


Microglia play a crucial role in the neuroinflammatory processes underlying a wide array of brain pathologies and are increasingly becoming targeted by drug discovery efforts.

The Microglia & Neuroinflammation Full-Pipeline service employs the Translucence Biosystems’ modified iDISCO+ tissue clearing protocol and AI-powered quantification pipeline, to provide microglia identification and inflammatory state quantification across entire brains. This service is suited for studies investigating diseases like Alzheimer's Disease.

Whole-brain microglial activation data provide insights into neuroinflammation underlying brain pathologies and pharmacological treatments, supporting drug discovery efforts.

Learn more about obtaining insights into microglial and neuroinflammatory responses within the CNS on our science page.

Neuroinflammatory Diseases


Insights into neuroinflammatory response within the CNS

Experimental Treatments That Impact Neuroinflammation

Perform behavioral, pharmacological, genetic, or other manipulation, and send us your samples. Or collaborate with us, and we’ll perform the animal treatments for you.

Tissue Clearing and Labeling of Microglia

We’ll use our modified iDISCO+ tissue clearing protocol to render intact samples optically transparent while also labeling microglia across the whole sample with a validated antibody against Iba1.

Light Sheet Imaging of Microglia Activation

Cleared and labeled samples are imaged on the Lightsheet Z.1 equipped with the Mesoscale Imaging System™. The Mesoscale Imaging System™ is optimized for imaging large intact tissues with unprecedented speed and resolution and is compatible with the high refractive index solutions used in tissue clearing protocols.

Translucence’s imaging pipeline captures cellular-resolution images of microglia, providing comprehensive insights into the distribution and intensity of the neuroinflammatory response induced by your experimental manipulation.

Stitching of Light Sheet Images

We employ our in-house developed software solution, Stitchy, for automated light sheet image stitching. Stitchy is a robust software solution that stitches large imaging datasets 2.5-5.5 times faster than leading commercial software solutions. By eliminating intermediate file formats, Stitchy enables seamless integration with downstream image analysis pipelines.

AI-Powered Whole-Brain Identification of Microglia

The Translucence Teravoxel Toolkit (3TK) software applies AI-powered algorithms to identify and segment individual microglia throughout the brain. AI-powered identification and segmentation workflows provide quantitative measurements of microglial density, morphology, and activation state, offering insights into immune responses within the CNS.

Actionable data

Browse actionable insights generated by the

Neuroinflammatory Diseases


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.

Colocalization of Microglia and Amyloid Plaques in 5xFAD Mice

In WT mice, individual homeostatic microglia are spaced out and have a ramified morphology with processes surveying the surrounding region. In diseased and inflamed states, activated microglia take on a condensed morphology. In 5XFAD Tg mice, microglia move to colocalize with B-amyloid plaques. Our automated methods can identify and count plaques and plaque-associated microglia (PAM) 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.

Brain-Wide Imaging of Microglia Activation Using iDISCO+ and Iba1 Staining

Exemplar optical slices from whole-brain immunostaining of microglia with an anti-Iba1 antibody. Brighter and more condensed microglia indicate there is activation throughout the brain when mice are treated with the inflammation-inducing agent, LPS.

The Neuroinflammatory Diseases Full-Pipeline Service

The Neuroinflammatory Diseases Full-Pipeline service is an end-to-end service that leverages next-generation 3D histology technologies encompassing tissue clearing, light sheet imaging, and AI-powered quantification to provide comprehensive insights into neuroinflammatory response within the CNS.

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