Whole organ 3D imaging

Obtain unique endpoints with Gubra 3D imaging platform

Light sheet microscopy and whole organ immunohistochemistry are revolutionizing our understanding of disease progression and drug distribution.  Gubra has implemented these novel technologies into our existing pre-clinical platform and now offers 3D imaging of intact organs with single cell resolution.

3D imaging is particularly useful when studying complex structures such as the vasculature or neuronal innervation. By injecting fluorescently labelled molecules, such as peptides or antibodies, you can also use the technology to visualize distribution throughout the body and in particular how they access the CNS.


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Main offerings

Drug induced neuronal activation
  • Whole brain cFos
  • Unbiased quantification

See video and flyer below

  • Neuron and fiber loss
  • Plaque and Tangle volume
  • Brain atrophy

See video and flyer below

Drug distribution
  • Peptides
  • Small molecules
  • Antibodies

Download flyer: Whole-organ drug distribution

  • Glomerular volume
  • Glomerular volume/distribution

See video and flyer below

Heart and vasculature
  • Ventricular volume
  • Capillary density

See video and flyer below

  • Beta cell mass
  • Beta cell proliferation
  • Islet number and islet volume

See video and flyer below

Other applications
  • NASH
  • Retinopathy
  • Adipose tissue
  • Glomerular function
  • Receptor mapping

Gubra 3D Experience

To enable fast and efficient data mining of quantitative 3D imaging data, Gubra has developed a web-based 3D imaging data viewer (Gubra 3D Experience, G3DE). This resource provides researchers with a platform for exploring Gubra’s published 3D imaging data in further detail.

Click here to explore individual brain regions of interest, display quantitative c-Fos data and filter for regions with statistically significant response to drug treatment.

Whole brain cFos

Using a novel reference atlas and improved c-Fos detection algorithms, Gubra offers an unbiased, automated and fast quantitative analysis of drug-induced c-Fos expressions across the whole mouse brain (video left).

For more information on our methods:

See animation: Drug induced c-Fos

Download flyer: 3D imaging of drug effects in the brain

A mouse brain atlas for virtual neuroscience

NeuroPedia is our vision of neuroscience in the future. It is an open source database for digital whole-brain maps recorded using light-sheet microscopy. The underlying principle is that all maps registered to the same reference brain are compatible. This will allow researchers to share and compare data from different experiments or overlay gene expression data with neuronal activity or connectivity – virtually!

Gubra Video Gallery

Gubra offers state-of-the art 3D imaging technologies to visualize pathogenesis and compound distribution in whole organs with single
cell resolution.

We have created a video gallery with a collection of all our favorite 3D imaging and stereology videos.


Deep learning computational analysis is applied for kidney-wide quantitation of glomerular volume and numbers (following in vivo administration of flouro-labelled lectin) and other renal structures of interest. Send us the kidney – our 3D imaging platform is applicable to any relevant in vivo kidney disease model (video right).

For more information on our methods:

See animation: Glomerular numbers and volumes

Download flyer: Whole-kidney morphometrics


High resolution imaging and deep learning computational analysis enables unbiased quantification of cardiovascular morphological changes, including ventricular volume, capillary density and atherosclerotic plaque volume (video left).

Send us the hearts. Our 3D imaging platform is applicable to any relevant in vivo heart disease model.

For more information on our methods:

See animations: LAD endpoints and Plaque burden 

Download flyers: 3D quantitation ofcardiovascular disease  and 3D quantitation of atherosclerosis


Light-sheet fluorescence microscopy allows for 3D imaging, mapping and quantification of the whole pancreas organ, including complete and unbiased quantifications of beta cell volumes and total number of islets (video left).

Send us the pancreas – our 3D imaging platform is applicable to any relevant in vivo pancreas disease model.

For more information on our methods:

See animation: Islet numbers and volumes

Download flyer: 3D assessment of beta cell mass


In animal models of Parkinson Disease (PD) estimation of dopaminergic neuron numbers and projections are imperative for model phenotyping and assessment of drug treatment effects (video right).

Send us the brains. Our 3D c-Fos imaging platform is applicable to any relevant in vivo model in the mouse.

For more information on our methods: 

See animation: A mouse model of Parkinson’s disease

Download flyer: Whole-brain analysis of dopaminergic cells