Evidence map›Paper›PMID 42244717›Full record

ArticlebioRxiv : the preprint server for biology2026

STIMscope: centimeter-scale all-optical imaging and patterned optogenetic manipulation at single-cell resolution.

Hamid Chorsi, Saray Soldado-Magraner, Yan Jin, Imaan Soltanalipouryekesammak, Alex Zheng, Dejan Markovic, Daniel H Geschwind, Peyman Golshani, Dean V Buonomano, Daniel Aharoni

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Hamid ChorsiDepartment of Neurology, University of California, Los Angeles, Los Angeles, CA, USA.ORCID 0009-0005-3634-5419
Saray Soldado-MagranerDepartment of Neurobiology, University of California, Los Angeles, Los Angeles, CA, USA.
Yan JinDepartment of Neurology, University of California, Los Angeles, Los Angeles, CA, USA.
Imaan SoltanalipouryekesammakDepartment of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
Alex ZhengDepartment of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA.
Dejan MarkovicDepartment of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
Daniel H GeschwindDepartment of Neurology, University of California, Los Angeles, Los Angeles, CA, USA.
Peyman GolshaniDepartment of Neurology, University of California, Los Angeles, Los Angeles, CA, USA.
Dean V BuonomanoDepartment of Neurobiology, University of California, Los Angeles, Los Angeles, CA, USA.
Daniel AharoniDepartment of Neurology, University of California, Los Angeles, Los Angeles, CA, USA.ORCID 0000-0003-4931-8514

Funding

Closed-Loop Systems for Large Scale Spatiotemporal Imaging and Actuation of Neural Activity in Freely Behaving AnimalsU01NS126050 · NINDS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI AHARONI, DANIEL, BLAIR, HUGH T · 2022 to 2025
$2.6M
Developing long-term neuro-behavioral recording and real-time processing platforms for naturally behaving animalsDP2MH129986 · NIMH · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI AHARONI, DANIEL · 2021 to 2024
$2.3M
Linking the dopaminergic mechanisms of reinforcement learning and timingR01DA060229 · NIDA · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI DEAN V BUONOMANO, Sotiris Masmanidis · 2025 to 2026
$1.2M
NIDA NIH HHS R01 DA060229NIMH NIH HHS DP2 MH129986NINDS NIH HHS U01 NS126050
6 · The paper itself

Abstract

Linking observation to intervention at cellular resolution makes it possible to move from measuring network activity to testing the contribution of defined neurons or ensembles within the same preparation. All-optical probing provides this capability by combining fluorescence-based readout with targeted optogenetic manipulation. Yet the platforms that deliver this capability remain complex, expensive, and difficult to maintain, requiring specialized expertise that has confined them to a small number of laboratories. They also typically provide fields of view too limited for studies of large, distributed neuronal populations. We address these constraints with the Spatiotemporal Illumination Microscope (STIMscope), a one-photon benchtop platform that integrates large-aperture tandem optics with a small-pixel back-illuminated CMOS sensor, a digital micromirror device for patterned illumination, and a GPU-based processing unit coordinated by a microcontroller for hardware-level synchronization. Ray-tracing simulations and point-spread-function measurements confirm cellular-scale resolution, with imaging lateral FWHM of 5.6 μm at the field center and 5.8 μm at the edge, and excitation lateral FWHM of 5.8 μm at the center and 6.2 μm at the edge, supporting fields of view as large as 14 mm × 11 mm in the demagnified configuration. The accompanying Closed-loop ready Real-time Imaging and Stimulation Pipeline (CRISPI) provides GPU-accelerated calibrated mask projection (26.3 ms latency), online ROI trace extraction, and modular ZeroMQ-based control, with a measured imaging-to-stimulation loop benchmark of 91.6 ms. We validate STIMscope in fixed mouse brain tissue, live iPSC-derived human neuronal cultures, and

Identifiers

PMID42244717
PMCPMC13232196

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.