800+
Brain regions
LS-JOURNEY™ FROM SAMPLE TO INSIGHT
The complete end-to-end platform for quantitative 3D mouse brain imaging, combining whole brain immunolabeling, light sheet microscopy, and AI-assisted image analysis. Use every module or only the steps you need.
PLATFORM DEFINITION
LS-JOURNEY™ (LIGHT SHEET JOURNEY)
A modular preclinical imaging platform that transforms a mouse brain sample into a complete, quantitative 3D dataset covering every anatomical region simultaneously, with AI-automated cell detection, atlas registration, and interactive delivery.
~1TB
Data per brain
Quantitative
AI-assisted analysis
2D+3D
Interactive data
PLATFORM OVERVIEW
FOUR MODULES.
ONE INTEGRATED PLATFORM.
Each module can be used independently or combined. The platform is designed so that the output of each step feeds directly into the next, but you can enter or exit at any point.
Module 01
Whole brain immunolabeling
3D IHC staining of intact mouse brains and optical tissue clearing using iDISCO. Compatible markers include c-Fos, CD31, aSMA, pSTAT3, GFP, RFP and custom antibodies.
Standalone use: receive cleared, stained brains returned to your lab.
Module 02
Light sheet microscopy
Full 3D acquisition of cleared brains at cellular resolution using light sheet fluorescence microscopy. Generates ~1 TB of raw image data per brain sample.
Standalone use: imaging of externally labelled and cleared samples.
Module 03
AI-assisted image analysis
Deep learning cell detection, signal quantification, and CCF atlas registration. Delivering quantitative results for 800+ brain regions via CNS-Voyager™.
Standalone use: analysis of your raw data and upload to CNS-Voyager™.
Add on
Study & regulatory reports
Scientific study reports and IND-enabling regulatory reports available on request for any module combination. Suitable for FDA/EMA submissions.
Available on request: on any study, any module combination.
VIBRAINT PRODUCT SERIES · EPISODE 1
LS-Journey™ explained. From tissue to virtual brain, with Jacob Hecksher-Sørensen
Hosted by Harry Salt (neuroscientist & life sciences content creator) · Guest: Jacob Hecksher-Sørensen, CEO & Co-founder, Vibraint · Topics: what LS-Journey™ is · the modular service model · how data is delivered · open science with CNS-Voyager™ · global logistics · the virtual brain vision
Available on Spotify & YouTube
Jacob Hecksher-Sørensen
Co-founder &
CEO at Vibraint
CEO at Vibraint
"Because this data is so rich. There's so much data. You can almost only view it in an online platform. Here you can scroll through the brain in any dimension you want and look up any brain region. You have the whole data at your hands."
-Jacob Hecksher-Sørensen, Vibraint
"One of the main goals for whole brain imaging is that you want to have an unbiased view of what happens. Maybe the most interesting effects you see are actually not where you initially thought you would see something."
-Jacob Hecksher-Sørensen, Vibraint
"Our hope is that once you have finalised the study and published the data, you make your maps available in the open access part of the viewer, so everybody can have a look and get inspired from those data sets."
-Jacob Hecksher-Sørensen, Vibraint
Module 01
WHOLE BRAIN IMMUNOLABELING
Whole brain immunolabeling combines optical tissue clearing with three-dimensional immunohistochemistry (IHC) to label specific proteins throughout an entire intact mouse brain. Rather than cutting the brain into 20–40 µm sections and examining a handful of pre-selected regions, this technique captures every labelled cell across all 800+ anatomical regions simultaneously: All in a single, unbiased 3D experiment.
The brain must first be processed to remove lipids. Primary antibodies then diffuse through the full tissue volume over 7–8 days at 37°C before secondary fluorescent antibodies complete the labelling. The result is a cleared, fluorescently-labelled brain ready for light sheet imaging.
Traditional IHC sectioning
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10–15 regions sampled
Pre-selected. Sampling bias unavoidable -
Brain destroyed
Sections cut. 3D spatial context permanently lost -
Manual counting
Weeks of work per brain. Observer-dependent
Whole brain immunolabeling
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800+ regions simultaneously
Zero bias. All brain regions captured at once -
Intact 3D volume
Full spatial context. Anatomy preserved in 3D -
AI assisted quantification
Every cell detected automatically. Reproducible
iDISCO+
Methanol dehydration → DCM delipidation → DBE refractive-index matching. Fast, high transparency. Gold standard for whole brain antibody-based IHC.
- Best for c-Fos, CD31, aSMA, Iba1, TH, MBP, NF, pSTAT3
- Turnaround ~4 weeks
- Note: Not suitable for endogenous fluorescence
Click here for more information about tissue processing and access to Vibraint's iDISCO protocol
COMPATIBLE MARKERS
iDISCO+ is compatible with a broad range of fluorescent markers used in preclinical neuroscience. Immediate early genes (IEGs) such as c-Fos, Arc, Egr1, and FosB are among the most widely used, reporting neuronal activity following pharmacological or behavioural stimuli. Cell-type markers enable brain-wide quantification of specific populations: NeuN for mature neurons, TH for dopaminergic neurons, ChAT for cholinergic neurons, Iba1 for microglia, and parvalbumin or calbindin for inhibitory interneuron subtypes. Signalling and phosphorylation markers, including pSTAT3, pERK, and pCREB. Receptor activation pathways are particularly valuable for drug mechanism-of-action studies. Structural markers such as MBP and Neurofilament allow whole-brain mapping of myelin and axonal architecture, while vascular markers including CD31 enable cerebrovascular mapping. For disease pathology, beta-amyloid, phospho-tau, and alpha-synuclein have been applied in Alzheimer's and Parkinson's models. For transgenic reporter lines expressing GFP, RFP, or their derivatives, native fluorescence is partially quenched during iDISCO+ processing, but the signal can be reliably recovered by immunostaining with anti-GFP or anti-RFP antibodies, preserving the full benefits of whole-brain 3D imaging.
Immediate early genes
Neuronal activity/inhibition mapping
c-Fos, pPDH, Arc, Egr1, FosB
Cellular markers
Markers against specific cell types
TH, Iba1, NeuN, ChAT
Activated signalling pathways
Receptor activation pathways
pSTAT3, pERK, pCREB
Transgenic reporters
Connectivity and genetic reporters
GFP, RFP, tdTomato, mCherry
Vascular/Structural
Architecture mapping
CD31, aSMA, MBP, NF
Diseases
Markers of disease pathology
aBeta, aSyn, pTau
At Vibraint, we are always looking to push the boundaries of whole brain imaging. If you have a custom marker you would like to explore, we welcome the opportunity to collaborate.
Module 02
LIGHT SHEET FLUORESCENCE
MICROSCOPY
Light sheet fluorescence microscopy (LSFM) illuminates the cleared brain with a thin laser sheet. One plane at a time. A camera positioned perpendicular to the light sheet captures the fluorescent signal from that plane, and the brain is scanned through the full volume to build a complete 3D image stack at single cell resolution.
Unlike confocal microscopy, which scans point-by-point, LSFM illuminates and captures entire planes simultaneously, making it orders of magnitude faster and causing minimal photobleaching. A full mouse brain can be imaged in hours rather than days.
The result is approximately 1 terabyte of raw image data per brain. A dataset so large that most research institutions lack the storage, computing infrastructure, and analysis pipelines to process it independently. This is the gap that LS-Journey™ Modules 02 and 03 address together.
Module 02 standalone service
Vibraint can image externally cleared brain samples. You can also submit your own raw light sheet data for AI analysis in Module 03, without engaging Module 02.
Setting up the microscope
The optically transparent brain from Module 01 is mounted in an imaging chamber filled with a refractive-index matching medium (ECi or equivalent) that matches the microscope objective.
Plane-by-plane laser sheet illumination
A thin sheet of laser light (typically 3–5 µm) illuminates one optical plane of the brain at a time. The illumination sheet is perpendicular to the detection axis. Only the focal plane fluoresces, minimising out-of-focus background.
Wide-field camera captures the plane
A wide-field sCMOS camera captures the full illuminated plane in a single frame or in multiple tiles, making acquisition orders of magnitude faster than point-scanning confocal methods.
Z-stack builds complete 3D volume
The brain is scanned through its full depth (~10 mm), building a complete 3D image stack at cellular resolution. Raw output: ~1 TB of image data, passed to Module 03 for AI analysis.
Module 03
AI-ASSISTED IMAGE ANALYSIS
One terabyte of raw light sheet images contains millions of individually labelled cells distributed across hundreds of brain regions. Extracting quantitative, reproducible numbers from this data by hand is practically impossible. LS-Journey™ Module 03 uses deep learning AI pipelines to automate every step of the analysis, producing publication-ready quantitative results.
Every dataset is registered to Vibraint's published mouse brain Common Coordinate Framework (CCF), a peer-reviewed 3D reference brain atlas that enables consistent anatomical mapping across samples, cohorts, and imaging modalities. The CCF was developed and published in Neuroinformatics by Vibraint founders Johanna Perens and Jacob Hecksher-Sørensen.
Results are delivered online via CNS-Voyager™, Vibraint's interactive 3D brain platform. Here researchers can explore their data, overlay public datasets (connectivity, transcriptomics, activity), and export figures for publication.
Module 03 standalone service
Submit your externally acquired light sheet dataset (from any instrument) for AI analysis and CCF registration. Results delivered via CNS-Voyager™.
Paper 1:
Perens et al., 2021. An Optimized Mouse Brain Atlas for Automated Mapping and Quantification of Neuronal Activity Using iDISCO+ and Light Sheet Fluorescence Microscopy. Neuroinformatics
.
Paper 2:
Perens et al., 2023. Multimodal 3D Mouse Brain Atlas Framework with the Skull-Derived Coordinate System. Neuroinformatics
Deep learning cell detection
A trained deep learning model scans the 3D volume and detects individual fluorescently-labelled cells. Output: 3D coordinates and signal intensity for every detected cell across the full brain volume.
CCF atlas registration
The light sheet dataset is non-linearly registered to Vibraint's published 3D mouse brain CCF. This maps every detected cell to its correct anatomical region enabling region-specific quantification and cross-sample comparison.
Region-specific quantification
Cell counts and signal intensity are aggregated per anatomical region, producing quantitative results for all 800+ regions simultaneously. Outputs include cell density maps, activity heatmaps, and region-level statistical tables.
CNS-Voyager™ interactive delivery
All results delivered online via CNS-Voyager™, allowing 3D and 2D interactive brain exploration, stereotactic coordinate placement, public dataset overlays, and export of publication-ready figures. No software installation required.
Add-on services
STUDY REPORTS AND
IND-ENABLING REPORTS
Scientific study reports and regulatory-formatted IND-enabling reports are available as add-ons for any LS-Journey™ study, across any combination of modules.
Scientific study report
A complete scientific summary of your LS-Journey™ study, presenting the quantitative brain imaging data in a structured, publication-ready format authored by Vibraint's team of neuroscience imaging scientists.
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Narrative summary of key findings across brain regions
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Quantitative data tables. Cell counts per region, statistical analysis
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High-resolution figures and whole-brain activity maps
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Interpretation relative to the CCF anatomical framework
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Methods section describing the LS-Journey™ pipeline
IND-enabling regulatory report
A regulatory-formatted report for whole brain imaging data. Structured for inclusion in Investigational New Drug (IND) applications to the FDA, EMA, or equivalent regulatory authorities. Suitable for CNS drug development programs requiring preclinical brain imaging data.
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Systematically formatted per regulatory documentation standards
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Complete methodology documentation
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Structured quantitative brain imaging data, target engagement, off-target activity
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Documentation of QC steps
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Statistical analysis and between-group comparisons
WHAT YOU RECEIVE
COMPLETE DATA DELIVERABLES
ACROSS ALL MODULES.
A full LS-Journey™ study delivers every output below. Individual modules deliver their respective subset. You choose the combination.
Anatomical segmentation
All 800+ mouse brain regions identified and labelled per the CCF. A reproducible structural framework across your cohort.
Quantitative cell counts
Region-specific counts for all labelled cell populations and signal intensities. Exportable tables, heatmaps, and statistical-analysis-ready data files.
Whole-brain activity maps
Immediate early genes (IEGs). Quantified across the full brain, CCF-registered for direct cross-sample and cross-cohort comparison.
CNS-Voyager™ 3D viewer
Interactive online brain exploration. 3D and 2D navigation, stereotactic coordinates, region lookup, figure export.
Multi-modal integration
Overlay your data with Allen Brain connectivity, spatial transcriptomics, and public activity datasets. All in the same reference space.
Publication-ready outputs
High-resolution brain figures, statistical summaries, and data exports formatted for peer-reviewed neuroscience journals.
Study report (on request)
Scientific narrative summary of findings, quantitative tables, figures, and statistical interpretation. Authored by Vibraint scientists.
IND report (on request)
Regulatory-formatted report for FDA/EMA IND submissions.
FREQUENTLY ASKED QUESTIONS
WHAT RESEARCHERS ASK
ABOUT LS-JOURNEY™
Comprehensive answers covering all modules
What is LS-Journey™?
LS-Journey™ is Vibraint's modular whole brain imaging platform for mouse models, combining whole brain immunolabeling (optical clearing and 3D IHC staining), light sheet fluorescence microscopy, and AI-assisted image analysis with CCF atlas registration. Results are delivered interactively via CNS-Voyager™. Each module can be used independently or combined. Study reports and IND-enabling regulatory reports are available as add-ons for any study.
What is whole brain immunolabeling and how does it compare to traditional IHC?
Whole brain immunolabeling combines optical tissue clearing with 3D IHC to label proteins across an intact mouse brain, capturing all 800+ regions in a single unbiased experiment. Traditional IHC sections the brain and samples 10–15 pre-selected regions, introducing sampling bias, destroying 3D spatial context, and requiring weeks of manual counting. Whole brain immunolabeling eliminates all three limitations.
How does light sheet fluorescence microscopy work?
Light sheet microscopy illuminates one plane of a cleared brain at a time with a thin laser sheet. A perpendicular camera captures each plane as the brain is scanned through its full depth, building a 3D volume at cellular resolution. This generates ~1 TB of raw data per brain with minimal photobleaching. Acquisition takes hours rather than days, making whole-brain cellular-resolution imaging practical for large studies.
How does LS-Journey™ AI-assisted image analysis work?
Deep learning algorithms automatically detect and count every labelled cell in the 3D light sheet volume. The dataset is then registered to Vibraint's published mouse brain CCF, mapping each detected cell to its anatomical region. Output includes quantitative cell counts for 800+ regions, whole-brain activity maps, and anatomical segmentation. All delivered via CNS-Voyager™.
What is the CCF mouse brain atlas used in LS-Journey™?
Vibraint uses a light sheet Common Coordinate Framework (CCF) developed by founders Johanna Perens and Jacob Hecksher-Sørensen and published in Neuroinformatics (link). This peer-reviewed 3D atlas enables reproducible anatomical registration across all samples, cohorts, and imaging modalities.
Is LS-Journey™ modular and can I use individual steps?
Yes. LS-Journey™ is fully modular. You can use the complete pipeline or individual modules independently. For example: Vibraint can perform AI analysis on your own externally acquired light sheet data (Module 03 only); or clear and stain your brains and return them to your lab for imaging (Module 01 only). Study reports and IND-enabling reports can be added to any combination.
Which IHC markers are compatible with LS-Journey™?
Compatible markers include immediate early genes (c-Fos, pPDH), cell-type markers ( Iba1, TH, ChAT, Parvalbumin), signalling markers (pSTAT3, pERK), transgenic reporters (GFP, tdTomato, mCherry), and structural markers (CD31, MBP, NF). Custom antibody targets can be validated on request. Contact Vibraint at the quote stage.
READY TO DESIGN YOUR WHOLE BRAIN STUDY WITH LS-JOURNEY™
Tell us your target markers, mouse model, sample numbers, and reporting needs and our scientists will design the optimal module combination and provide a detailed quote.