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Optogenetics App
The Optogenetics App (and Optogenetics Pro) by PopNeuron is a free iOS and Android application that calculates required laser power for in-vivo optogenetic experiments. Using a validated light-scattering model calibrated across seven mouse brain areas, it outputs penetration depth as a function of optical power for any brain region, opsin, and fiber combination—essential for planning effective and safe optogenetic stimulation.
What is the Optogenetics App?
The Optogenetics App (and companion Optogenetics Pro) from PopNeuron is a free mobile application that calculates the optical power requirements for in-vivo optogenetic experiments. Designing an effective optogenetic experiment requires accurate knowledge of the light-scattering properties of the target brain region, the opsin being used, and the optical fiber characteristics. Without proper calculations, investigators risk under- or over-stimulating their target, wasting experiments or harming tissue. The Optogenetics App solves this with a validated mathematical framework and an integrated brain atlas.
How It Works
The investigator inputs the target brain area, the opsin of interest, and the optical fiber parameters. The app calculates the maximal depth at which the chosen opsin can be excited under those conditions, and displays the penetration depth as a function of optical power (in mW). The underlying model was validated through empirical light-scattering measurements in live mouse brain tissue across seven brain areas and whole-brain imaging under blue light (470 nm), yielding a calibrated mathematical framework that extrapolates accurately to other brain regions.
Version 4.0 (2025)
Version 4.0 was completely rebuilt from the ground up in 2025 on modern software platforms, providing full compatibility with current iPhone, iPad, and Android devices. Both Optogenetics and Optogenetics Pro versions are now functionally identical—the historical distinction (atlas plate count) is no longer relevant given modern smartphone storage. Both versions remain available in their respective stores to avoid disrupting links for existing users.
Key Features
- Precise Light Power Calculation: Calculates required optical power based on brain region scattering coefficients, opsin sensitivity, and fiber properties.
- 17 Opsins Supported: Compatible with all major channelrhodopsins and inhibitory opsins across common excitation wavelengths.
- Integrated Brain Atlas: Full adult mouse brain atlas (43 high-resolution plates in Pro) or simplified 5-plate atlas (regular version).
- Visual Output: Graphical penetration depth vs. optical power plot for intuitive experimental planning.
- Free Download: Available at no cost from the Apple App Store and Google Play Store.
- Validated Model: Calibrated against empirical measurements across seven distinct brain areas in live mouse tissue.
Applications
- Planning in-vivo optogenetic neuron activation or silencing experiments
- Estimating required laser or LED power for fiber photometry studies
- Optimizing light delivery parameters for any brain region and opsin combination
- Teaching and training in optogenetics experimental design
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Technical Specifications
| Product | Optogenetics App / Optogenetics Pro |
| Version | 4.0 (2025) |
| Platform | iOS (iPhone, iPad) and Android |
| Price | Free download |
| Opsins Supported | 17 channelrhodopsins and inhibitory opsins |
| Brain Atlas (Regular) | 5 atlas plates, ~74 MB install size |
| Brain Atlas (Pro) | Full adult mouse brain atlas, 43 high-resolution plates, ~430 MB install size |
| Output | Optical power (mW) vs. penetration depth graphical plot |
| Validation Method | Empirical light-scattering measurements in live mouse brain tissue, calibrated across 7 brain areas |
| Distributed By | PopNeuron LLC (licensed from University of Colorado) |
| App Store Availability | Apple App Store and Google Play Store |
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The Optogenetics App is licensed from the University of Colorado and based on published light-scattering models validated empirically across seven mouse brain areas, with the underlying technology cited across dozens of optogenetics studies.
What is the Optogenetics App and what problem does it solve?
The Optogenetics App (and Optogenetics Pro) from PopNeuron is a free mobile application that calculates the optical power requirements for in-vivo optogenetic experiments using light delivered via implanted optical fibers. Without accurate power calculations, investigators risk ineffective stimulation or tissue damage. The app solves this by modeling light scattering based on the specific optical properties of the target brain region, the chosen opsin, and the fiber parameters.
What is the difference between the Optogenetics App and Optogenetics Pro?
In the current version (4.0), both apps are functionally identical. The distinction originated when smartphone storage was limited: the Pro version included more brain atlas plates. With modern devices, both versions include the same calculations and the full adult mouse brain atlas. Both are maintained in the Apple App Store to avoid breaking links for existing users; the Google Play Store carries only the Optogenetics version.
How accurate are the calculations in the Optogenetics App?
The app's mathematical model was validated by measuring light scattering in live mouse brain tissue using optical fibers moved through multiple brain areas, and by imaging an entire mouse brain under blue light (470 nm) within a calibrated grayscale setup. Results were calibrated across seven brain areas. Scattering coefficients for other regions are extrapolated from these validated data points and fit well within the established calibration curve.
What opsins and brain regions does the app support?
The Optogenetics App supports 17 different opsins across common excitation wavelengths. The Pro version includes a full adult mouse brain atlas with 43 high-resolution plates, allowing users to look up and mark any target brain region. The regular version includes 5 commonly used atlas pages. Light scattering coefficients are available for validated brain areas, with extrapolated values for additional regions.
Is the Optogenetics App available for use in Israel and does NBT Ltd provide support?
Yes. The Optogenetics App is a free download available globally from the Apple App Store and Google Play Store. NBT Ltd, as the authorized distributor of POPneuron in Israel, can provide guidance on integrating the app into your experimental workflow and on sourcing compatible hardware such as optical fibers, laser sources, and stereotaxic equipment.
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