SmartAnalytics

Powerful workstation for 3D image datasets

Optimized for terabyte-size 3D datasets from our SmartSPIM light sheet microscope, SmartAnalytics gives you in-house control of analysis and extensive computational power without having to code your own solution. Install SmartAnalytics on your own high-powered workstation, or let LifeCanvas provide you with a workstation optimized for this analysis pipeline with the software pre-installed.

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Bar plot showing detected c-FOS+ cells in different brain regions by treatment group
Detected c-FOS+ cells in different brain regions.
Heat maps showing c-FOS+ fluorescence intensity by treatment group
c-FOS+ fluorescence intensity.
Annotated coronal view of a mouse brain with Allen Brain Atlas overlay

Easy Allen Brain Atlas alignment

SmartAnalytics is designed for minimally-experienced users: you don’t have to be a computer scientist or expert neuroanatomist to produce a well-aligned dataset. Accurate alignment to the Allen Brain Atlas allows for precise cell counts and fluorescence localization measurements.

Publication-ready results

Generate accurate cell counts and fluorescence intensity outputs for highly granular brain regions, enabling multi-sample statistical significance testing. Export heat maps directly from the software, ready to be embedded into your next grant submission, presentation, or publication.

Adaptable cell detection models

Machine learning algorithms provide reliable cell detection for a variety of applications, including:

  • Neural activity: Detect and map c-FOS+ cells in whole brains for insight into brain regional activity levels unaffected by selection bias.
  • Endogenous fluorescence: Identify and quantify fluorescently-tagged cells throughout whole tissue volumes.
  • Neurological disease markers: Assess disease progression and expression, as well as neuroinflammatory response, with models for astrocytes (GFAP) and microglia (IBA1), and segmentation analyses for β-amyloid deposits (senile plaques) and α-synuclein aggregates (Lewy Bodies).
  • Other cell-type markers: Identify and quantify neurons immunolabeled for NeuN, TH, PV, and more.
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NeuN+ cell detection in mouse brain
NeuN+ cell detection
c-FOS+ cell detection in mouse brain
c-FOS+ cell detection

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Further reading

How to use the Allen Brain Atlas

The Allen Brain Atlas is an incredibly powerful tool for neuroscience research, enabling researchers to discuss their findings in a...