Pipeline

Pipeline A - Figure 1

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{{pipeline-a-1="/science-figures"}}

Whole Brain Smooth Muscle Actin Staining

This image shows a mouse brain stained for smooth muscle cells surrounding arteries using tissue-clearing and immunolabeling methods. This helps scientists visualize the blood-brain barrier, a critical barricade that limits the entry of therapeutics into the brain. This image was featured in the 2024 BRAIN Initiative Calendar.

Pipeline A - Figure 2

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{{pipeline-a-2="/science-figures"}}

Time Lapse of a Mouse Brain Clearing

Time Lapse of a Mouse Brain Clearing

Time-lapse video of the optical clearing step in Translucence’s tissue staining and clearing protocol. This brain is held in place with one of the tissue clamps that comes with the Mesoscale Imaging System.

Pipeline B - Figure 1

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{{pipeline-b-1="/science-figures"}}

Whole Brain Smooth Muscle Actin Staining

This image shows a mouse brain stained for smooth muscle cells surrounding arteries using tissue-clearing and immunolabeling methods. This helps scientists visualize the blood-brain barrier, a critical barricade that limits the entry of therapeutics into the brain. This image was featured in the 2024 BRAIN Initiative Calendar.

Pipeline B - Figure 2

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{{pipeline-b-2="/science-figures"}}

Kidney Smooth Muscle Actin

This kidney sample was stained with Smooth Muscle Actin (SMA) and prepared using Translucence Universal Tissue Clearing Kit, which in combination with your chosen antibodies, empowers you to effortlessly clear and stain an extensive range of tissues, including mouse brain, lung, liver, spinal cord, and more.

Pipeline B - Figure 3

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{{pipeline-b-3="/science-figures"}}

Visualization of Smooth Muscle Actin (SMA) in P7 (Postnatal Day 7) Mouse Lung

Visualization of Smooth Muscle Actin (SMA) in P7 (postnatal day 7) mouse lung. Staining intact lungs with SMA and other markers can provide pivotal insights into lung development and pathology.

Pipeline B - Figure 4

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{{pipeline-b-4="/science-figures"}}

Embryonic β-Tubulin Staining

Embryonic β-Tubulin Staining

Embryonic β-Tubulin staining showcases the intricate structure of a mouse embryo. This footage is brought to light using Light Sheet Fluorescence Microscopy (#LSFM) techniques, imaged on the ZEISS Lightsheet Z.1 equipped with the Mesoscale Imaging System™️. Sample preparation performed using our NIH-funded Universal Tissue Clearing Kit.

Pipeline C - Figure 1

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Image depicting Brain Vasculature created using the Translucence Universal Tissue Clearing Kit.

Arteries:

This image shows a mouse brain stained for smooth muscle cells surrounding arteries using tissue-clearing and immunolabeling methods. This helps scientists visualize the blood-brain barrier, a critical barricade that limits the entry of therapeutics into the brain. This image was featured in the 2024 BRAIN Initiative Calendar.

Pipeline C - Figure 2

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{{pipeline-c-2="/science-figures"}}
Image depicting Brain Vasculature created using the Translucence Universal Tissue Clearing Kit.

Time Lapse of a Mouse Brain Clearing

Time-lapse video of the optical clearing step in Translucence’s tissue staining and clearing protocol. This brain is held in place with one of the tissue clamps that comes with the Mesoscale Imaging System.

Pipeline D - Figure 1

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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.

Pipeline D - Figure 2

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VoxelsTM Workflow

Our Voxels software uses AI powered workflows to segments objects of interest across whole intact samples. Then, in the case of mouse brains, Voxels can warp each sample and their segmented objects to the Allen reference atlas to generate whole brain regional quantification of the epitope of interest.

Pipeline D - Figure 3

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Brain-Wide Quantification of Neuronal Activity Across Hundreds 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.

Pipeline D - Figure 4

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Time Lapse of a Mouse Brain Clearing

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 are portions of 3D microglia labels that project orthogonal to this 2D representation. Cell masks allow for counts, shape analysis, and fluorescence intensity measurements.

Pipeline D - Figure 5

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Time Lapse of a Mouse Brain Clearing

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.

Pipeline D - Figure 6

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Time Lapse of a Mouse Brain Clearing

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 β-amyloid plaques. Our automated methods can identify and count plaques and plaque-associated microglia (PAM) throughout the brain.

Pipeline D - Figure 7

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Time Lapse of a Mouse Brain Clearing

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.

Pipeline D - Figure 8

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Time Lapse of a Mouse Brain Clearing

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 areas, the data from our Amyloid and PAM whole-brain quantification workflows are strongly correlated.

Areas

Area A - Figure 1

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Time Lapse of a Mouse Brain Clearing

β-Amyloid Plaque Staining and Labels in an 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, immunoreactivity is measured with an anti-Amyloid antibody. On the right, our AI-powered workflow in our 3TK software identifies and labels aggregates throughout the brain.

Area A - Figure 2

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Time Lapse of a Mouse Brain Clearing

β-Amyloid Plaque Quantification

This figure shows a series of z-planes through an individual brain. The 2D heat maps demonstrate β-amyloid plaque density at various depths through a 5xFAD mouse brain, with areas of high plaque density highlighted in yellow, while areas of low plaque density are purple. Our VoxelsTM software quantifies β-amyloid plaque density across hundreds of brain regions. Data from a few brain regions in 3-month and 5-month old WT and 5x-FAD are shown above.

Area B - Figure 1

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Time Lapse of a Mouse Brain Clearing

Tyrosine Hydroxylase (TH) Staining of a Whole Mouse Brain

Tyrosine Hydroxylase (TH) staining of a whole mouse brain visualizes the distribution of dopamine, norepinephrine, and epinephrine-containing (catecholamine) neurons and endocrine cells. TH is a key enzyme involved in neurotransmitter production. Immunohistochemical detection of TH expression is one tool for visualizing and quantifying damage and loss of dopaminergic neurons, involved in disorders including Parkinson’s disease. Sample imaging performed on the ZEISS Lightsheet Z.1 equipped with the Mesoscale Imaging System™.

Area B - Figure 2

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Time Lapse of a Mouse Brain Clearing

Brain-Wide Quantification In Mice Injected with α-Synuclein Preformed Fibrils (Pff)

Area B - Figure 3

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Time Lapse of a Mouse Brain Clearing

Whole-Brain Visualization of Tyrosine Hydroxylase Distribution

Volume quantification tool used on in-house 3D Tyrosine Hydroxylase staining. Our newly developed volume quantification tool does not segment individual objects, but measures the total fluorescence in each brain region. Because TH staining is very different in different brain regions, segmentation is problematic, so we used this new tool to calculate TH integrated intensity across hundreds of brain regions.

Area C - Figure 1

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Time Lapse of a Mouse Brain Clearing

Whole-Brain Immunostaining of Iba1(+) Microglia

Intact mouse brains from experimental animals are removed and processed with Translucence's optimized iDISCO-modified protocol. After immunostaining with an anti-Iba1 antibody, imaging in the Mesoscale Imaging SystemTM and processing with our light sheet image stitching software, StitchyTM, large terabyte-scale image files reveal microglia throughout the entire brain. This figure shows zoomed regions from 2D optical slices at various plane depths in a single brain.

Area C - Figure 2

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Time Lapse of a Mouse Brain Clearing

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, lipopolysaccharide (LPS).

Area C - Figure 3

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Time Lapse of a Mouse Brain Clearing

AI-Powered Microglia Shape and Count Workflows

We trained AI-powered 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.

Area C - Figure 4

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Time Lapse of a Mouse Brain Clearing

Brain-Wide Quantification of the Inflammatory Response to Coronavirus

Area C - Figure 5

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Time Lapse of a Mouse Brain Clearing

Spinal Cord Inflammation Caused by Coronavirus Infection

Area C - Figure 6

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Time Lapse of a Mouse Brain Clearing

Regionally Localized Neuroinflammatory Response to Infection with a Murine Coronavirus

The images on the left show optical slices through a control brain and a brain treated with the murine coronavirus, MHV (murine hepatitis virus). A large neuroinflammatory response is induced by viral treatment, with clear regional patterns of microglial activation.

Area C - Figure 7

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Time Lapse of a Mouse Brain Clearing

Colocalization of Microglia and β-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 β-amyloid plaques. Our automated methods can identify and count plaques and plaque-associated microglia (PAM) throughout the brain.

Area C - Figure 8

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{{area-c-8="/science-figures"}}

Time Lapse of a Mouse Brain Clearing

Time Lapse of a Mouse Brain Clearing

In 5XFAD mice, Iba1 (+) microglia colocalize with β-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 β-amyloid levels detected in the same mice. Across hundreds of brain areas, the data from our β-amyloid and PAM whole-brain quantification workflows are strongly correlated.

Area D - Figure 1

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Time Lapse of a Mouse Brain Clearing

Simultaneous measurement of cFos and Npas4 throughout the brain, enabling cellular-resolution monitoring of recent neuronal activity-dependent signal transduction using the Translucence Neuronal Activity Tissue Clearing Kit.

Npas4 Expression is Exquisitely Tuned to Neuronal Activity

The immediate-early gene (IEG) cFos is widely used as a go-to marker for detecting neuronal activity. However, cFos is also regulated by cAMP and other paracrine factors, limiting its specificity as a pure marker of neuronal activity.

In contrast, the IEG Npas4 is exclusively regulated by calcium (Ca²+) signaling downstream of neuronal activity, providing a more precise readout of recent neuronal activity.

Simultaneous measurement of both immediate-early genes (IEGs), cFos and Npas4, provides researchers with a more robust and comprehensive picture of recent neuronal activity.

Area D - Figure 2

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Time Lapse of a Mouse Brain Clearing

Automated Identification of Npas4 and cFos Cells in iDISCO+ Cleared Brains

Optical slices through an intact mouse brain, cleared and stained with antibodies against cFos and Npas4 using our modified iDISCO+ procedure. Translucence Biosystems’ 3TK software uses machine learning and a series of deterministic filters to label immunoreactive neurons in 3D throughout the brain. The color labels are arbitrary to help distinguish individual neurons.

Area D - Figure 3

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Time Lapse of a Mouse Brain Clearing

Brain-Wide Quantification of Neuronal Activity across Hundreds of Brain Regions

These 2D spatial heatmaps are extracted 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 hundreds 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.

Area E - Figure 1

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Time Lapse of a Mouse Brain Clearing

Intravenous Administration of Monospecifc and Bispecific anti-BACE1 Antibodies

We dosed mice intravenously with various concentrations of a monospecific antibody targeting BACE1 or a bispecific antibody that is similar, but with the addition of a domain binding to the transferrin receptor (TfR1). The transferrin receptor is found in blood vessel endothelial cells where it acts as a carrier to transport iron. Antibodies binding to the transferrin receptor can hijack this mechanism to be transported across the blood-brain barrier.

Area E - Figure 2

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Time Lapse of a Mouse Brain Clearing

Staining Validation with Multiple anti-Human IgG Antibodies

When developing the methodology for whole-brain imaging of IV-dosed experimental therapeutic human antibodies, we tested multiple different secondary antibodies. The top panels show sagittal planes of intact brains stained with three different secondary antibodies. All three produced qualitatively similar results, but anti-Human IgG #3 had better brain penetration and more even whole-brain staining.  The images reveal bispecific Ab enriched in the blood vessels where it binds to the transferrin receptor, but also distribution across the BBB in the parenchyma.

Area E - Figure 3

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Time Lapse of a Mouse Brain Clearing

Enrichment of Bispecific Antibody Throughout the Brain

Our modified iDISCO+ protocol allows for imaging of an entire intact tissue, giving an unbiased snapshot of immunoreactivity throughout the brain. Consistent with the data from the hippocampus, we discovered that the monospecific antibody has negligible brain penetration, whereas the bispecific antibody is identified in both the vasculature and parenchyma throughout the brain. The bispecific BACE1 antibody is particularly enriched in a number of brain areas including the Pontine Gray, Medulla and Glomeruli in the Olfactory Bulb. This quantification includes both the vascular and parenchymal components of the signal.

Area E - Figure 4

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Time Lapse of a Mouse Brain Clearing

iDISCO Whole-Brain Imaging of IV-dosed anti-BACE1 Antibodies

24 hours after dosing, using our modified iDISCO+ protocol, we cleared and stained perfusion-fixed brains using an anti-human IgG secondary antibody. We could not detect any immunoreactivity in the brains of mice injected with the monospecific antibody, with background signals identical to brains from non-infected mice. With the bispecific antibody, strong staining was observed in blood vessels, and importantly, in the brain parenchyma.

Area F - Figure 1

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Time Lapse of a Mouse Brain Clearing

iDISCO Whole-Organ Imaging of Intact Mouse Liver

Tissue clearing and staining of whole mouse liver using an antibody against Smooth Muscle Actin (SMA) in Cyan and a bile duct-specific antibody in green. Light Sheet Fluorescence Microscopy (LSFM) imaging of vasculature and bile duct networks provides comprehensive insights into the 3D morphology of both targets.

Area F - Figure 2

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Time Lapse of a Mouse Brain Clearing

Pre- & Post-Segmentation of Liver Bile Ducts

On the left is the raw biliary tree signal from a P7 mouse liver, and on the right is an image of the segmented bile duct network.

Area G - Figure 1

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Time Lapse of a Mouse Brain Clearing

Image depicting Brain Vasculature created using the Translucence Universal Tissue Clearing Kit.

Time Lapse of a Mouse Brain Clearing

Time-lapse video of the optical clearing step in Translucence’s tissue staining and clearing protocol. This brain is held in place with one of the tissue clamps that comes with the Mesoscale Imaging System.

Area G - Figure 2

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Time Lapse of a Mouse Brain Clearing

Image depicting Brain Vasculature created using the Translucence Universal Tissue Clearing Kit.

Time Lapse of a Mouse Brain Clearing

Time-lapse video of the optical clearing step in Translucence’s tissue staining and clearing protocol. This brain is held in place with one of the tissue clamps that comes with the Mesoscale Imaging System.

Area G - Figure 3

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{{area-g-3="/science-figures"}}

Time Lapse of a Mouse Brain Clearing

Image depicting Brain Vasculature created using the Translucence Universal Tissue Clearing Kit.

Time Lapse of a Mouse Brain Clearing

Time-lapse video of the optical clearing step in Translucence’s tissue staining and clearing protocol. This brain is held in place with one of the tissue clamps that comes with the Mesoscale Imaging System.

Area G - Figure 4

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{{area-g-4="/science-figures"}}

Time Lapse of a Mouse Brain Clearing

Image depicting Brain Vasculature created using the Translucence Universal Tissue Clearing Kit.

Time Lapse of a Mouse Brain Clearing

Time-lapse video of the optical clearing step in Translucence’s tissue staining and clearing protocol. This brain is held in place with one of the tissue clamps that comes with the Mesoscale Imaging System.

Area G - Figure 5

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{{area-g-5="/science-figures"}}

Time Lapse of a Mouse Brain Clearing

Image depicting Brain Vasculature created using the Translucence Universal Tissue Clearing Kit.

Time Lapse of a Mouse Brain Clearing

Time-lapse video of the optical clearing step in Translucence’s tissue staining and clearing protocol. This brain is held in place with one of the tissue clamps that comes with the Mesoscale Imaging System.