Optogenetics for biosight

Optogenetic neuron stimulation is a widely used technique in neuroscience, both in vitro and in vivo in freely behaving or freely moving animals. See also optogenetic-axon-guidance for specific techniques to design and pattern neuronal networks. See optogenetics for a high-level overview.

Of particular interest is high resolution spatial light modulation to transmit information to neurons or cells. Retinal explants or retinal organoids are interesting options because they have extremely high density photoreceptors, rods, cones, and retinal ganglion cells leading into the axons bundle usually called the optic nerve. Each human eye has approximately 1.2 million axons in the optic nerve, and about 100 million sensors. There are some eagles with approximately 5 million retinal ganglion cells and corresponding axons in the optic nerve per eye.

A deep problem of neurosicence is that microelectrode arrays have not significantly scaled in size or density. Many millions of electrodes are needed for simultaneous read and write. Optogenetics or retinas can get us to 100 million or more 'electrodes' (sensors), and these sensors can be individually addressable depending on their geometry or spacing compared to our ability to deliver addressable input via spatial light modulation at the same acuity. Likewise, optogenetics can also deliver significantly high resolution high bandwidth output via motor neurons as actuators or even simple optogenetic genetically encoded optical voltage indicators monitored by light microscopy or fluorescence microscopy.

"Arrays of microscopic organic LEDs for high-resolution optogenetics" - ".. the arrays comprise 230,000 OLED pixels across an area of ~20 mm2 ... To harness the high resolution of the OLED microarrays and the unrestricted simultaneous switching of pixels for pattern generation, cells have to be in close proximity to the OLEDs; ideally, the separation is less than the pixel size. To enable close contact while still protecting the water-sensitive OLED materials from the aqueous cell culture environment, OLED arrays were protected by a thin-film encapsulation barrier consisting of alternating layers of Al2O3 and an organic Barix polymer (three layers of Al2O3 and two layers of polymer; total thickness, 1.5 μm; Vitex Systems)... " oh also it's lens-free.

"Optogenetic stimulation probes with single-neuron resolution based on organic LEDs monolithically integrated on CMOS"

Retinal organoids

Ex vivo retina explant (organotypic retina)

  • Vats et al., 2025 — Methods in Molecular Biology: step-by-step explant isolation/culture from mouse, human, and NHP, geared to drug testing & AAV work. PubMed
  • Schaeffer et al., 2020 — Frontiers in Molecular Neuroscience: adult mouse retina explants; practical tips (tissue orientation, cutting method) and how findings map back in vivo. Open access. PMC
  • Müller et al., 2017 — IOVS: survival/cellular changes in adult murine organ cultures up to 10 days; baseline morphology/markers. IOVS
  • Elmasry et al., 2022 — JoVE: video protocol for adult mouse retinal neurovascular explants (isolation, culture, staining). JoVE
  • Rossino et al., 2022 — Annals of Eye Science (review): where retinal explants fit for neurovascular disease modeling. Annals of Eye Science
  • Chan et al., 2024 — Acta Neuropathologica Communications: organotypic model preserving retinal cytoarchitecture; useful reference list to perfused-eye literature. BioMed Central
  • Yang et al., 2024 — Journal of Neuroscience Methods: compares static vs perfused culture conditions for retinal explant viability. ScienceDirect
  • Donovan et al., 2006 — Nature Protocols: classic organotypic retina culture & electroporation workflow (mouse/monkey/human developmental stages). PubMed

Ex vivo ocular whole-eye perfusion

  • Rousou et al., 2019 — Experimental Eye Research (technical protocol): arterially perfused porcine eyes; detailed setup mimicking human ocular anatomy/flow. ScienceDirect
  • Eltanahy et al., 2023 — Experimental Eye Research (open access): porcine whole-eye arterial perfusion for vascular function studies; stepwise build and validation. PMC
  • Zhou et al., 2017 — IOVS (ARVO abstract): compact, scalable whole-eye perfusion system validated on bovine/porcine eyes (higher-throughput screening). IOVS
  • Kutlehria et al., 2019 — Pharmaceutical Research (open access): whole-eye perfusion for drug delivery screening; permeability vs physicochemical properties. PMC
  • Chowdhury et al., 2025 — Methods in Molecular Biology: human anterior segment perfusion organ culture at physiological flow (2.5 µL/min) for outflow/IOP studies. PubMed
  • Mao et al., 2011 — PLoS One (open access): bovine anterior segment perfusion; steroid-induced myocilin & IOP elevation—glaucoma-relevant. PMC
  • Mao et al., 2023 — ARVO abstract: toward mouse anterior-segment perfusion for outflow facility & long-term culture. IOVS
  • Mains et al., 2012 — European Journal of Pharmaceutics & Biopharmaceutics: isolated perfused ovine eye for pharmacokinetics/distribution of ocular therapeutics. ScienceDirect
  • Kasetti et al., 2019 — ARVO abstract: ex-vivo human anterior segment to study glaucoma factors & IOP. IOVS
  • González-Fernández et al., 2025 — Scientific Reports: 3D-printed perfusion rig; porcine whole-eye maintained ≥18 h for lateral diffusion/drug testing. Nature

You can keep a native (ex vivo) retina alive in culture and even preserve the optic-nerve head (ONH) or a short optic-nerve stump; whole-eye perfusion models also exist. You can (i) culture native retina/ONH (optic nerve head) ex vivo, or (ii) build retina→thalamus→cortex “assembloids” entirely from organoids so RGC axons grow out of the retina (rather than bringing in an intact optic nerve).

What’s been done already

  • Adult retina organotypic/explant culture (rodent, human, NHP). Robust protocols maintain layered structure and RGCs for days–weeks; many labs culture whole-mount retina on membranes for physiology, imaging, AAV testing, etc. PMC
  • ONH/optic-nerve–preserving explants (in vitro). Groups report organotypic cultures that explicitly leave the ONH and a short optic-nerve segment intact, improving RGC integrity and enabling ONH studies. (Investigative Ophthalmology & Visual Science, 2023 abstract). IOVS
  • Whole-eye / ocular perfusion ex vivo. Mouse, porcine, and human whole-globe perfusion preparations preserve retinal cytoarchitecture and light responses for hours–day-scale windows (good for physiology/tox studies). PMC, BioMed Central
  • Ex vivo retina physiology with intact tissue. Ex vivo ERG on intact retinas (animal/donor) and compound action potential recordings from freshly dissected optic nerves are standard. Ophthalmology & Visual Sciences, PMC
  • Retina→brain organoid “assembloids” (all from stem cells). A landmark model fused retinal, thalamic (LGN-like), and cortical organoids; RGC axons extended deep into the thalamic/cortical targets and RGC survival improved in the long term. This is the cleanest demonstration of retinofugal projections in vitro, but it starts from organoids (no native optic nerve). PMC
  • Retina co-culture/target specificity models. Earlier work co-cultured RGCs or retinal tissue with thalamic/tectal targets to test targeting and synaptogenesis (again, generally new outgrowth, not plugging in an intact adult optic nerve). PMC

What hasn’t (apparently) been shown yet

  • A naturally developed retina + long, intact optic nerve transplanted into an organoid system and kept functionally connected through that native nerve. I couldn’t find a paper demonstrating stable long-term culture of the entire adult mammalian optic nerve in vitro and functional synaptic drive into a brain organoid via that nerve.

    The obstacles are well-known: adult RGC axons don’t spontaneously regrow; long myelinated CNS axons undergo Wallerian degeneration without perfusion and glial support; and guidance/lamination cues are needed to land in the correct thalamic layers. That’s why ex vivo retina models usually keep only a short ONH/nerve stump (for days–weeks), and why retinofugal assembloids rely on new axonal extension from RGCs. Frontiers

Feasible near-term bridge experiments (if you want to try this)

  • Start with ONH-preserving retina explants, placed close to a thalamic organoid or brain slice in a micro-device that bridges the gap (micro-tunnels/ECM strands). Add pro-regeneration cues (PTEN/SOCS3 modulation, CNTF, c-Myc) shown to enable adult RGC axon growth in optic-nerve injury models; monitor outgrowth with anterograde tracers and GEVI/GCaMP in the target. Frontiers
  • Alternatively, whole-eye perfusion coupled to an adjacent organoid chamber (shared medium/perfusion) could extend viability while you attempt short-range neurite bridging from the ONH stump; but expect days, not weeks, of stable function unless you move to an assembloid strategy. PMC, BioMed Central
  • If you mainly want a “natty retina front-end”, the most tractable path today is: native retina (ex vivo) for phototransduction + DMD patterned stimulation, and readout/processing in vitro via direct RGC recordings or optical voltage imaging—without insisting on using the native long optic nerve as the link. The “wired” link can be newly grown axons into a thalamic organoid, as demonstrated in the assembloid literature. PMC

Representative references

  • Adult retina explants / regeneration models: Schaeffer et al., 2020 (Frontiers in Mol. Neurosci.)—adult retina explants to study axon regeneration; methods & comparisons to in vivo optic-nerve injury. Frontiers
  • ONH-preserving organotypic culture: Wang et al., 2023 (IOVS abstract)—“optic-nerve–preserving culture helps preserve RGC integrity and allows ONH studies.” IOVS
  • Whole-eye perfusion: Eltanahy et al., 2023 (ex vivo mouse eye perfusion); Chan et al., 2024 (organotypic whole-globe perfusion, porcine & human)—retinal structure preserved up to \~24 h. PMC, BioMed Central
  • Ex vivo physiology: Vinberg et al., 2015 (ex vivo ERG from intact retinas); Bastian et al., 2020 (ex vivo optic-nerve CAPs). Ophthalmology & Visual Sciences, PMC

  • Retina→thalamus→cortex assembloid: Fligor et al., 2021 (Stem Cell Reports)—RGC axons extend into thalamic/cortical organoids; enhanced RGC survival. PMC

  • Holographic optogenetic stimulation of patterned neuronal activity for vision restoration

Bottom line: keeping a native retina + short ONH alive ex vivo is routine, whole-eye perfusion is feasible short-term, and retina→brain connections are best modeled today with organoid assembloids where RGCs regrow into the targets. A true transplant of a native retina with its long optic nerve into organoids hasn’t been shown yet, but you could prototype a hybrid system that preserves the native retina while encouraging new RGC outgrowth into thalamic/cortical organoids—combining the biological front-end you want with a tractable wiring strategy supported by current literature. Frontiers, PMC, IOVS, BioMed Central