STIMscope/CITATION.cff at main · Aharoni-Lab/STIMscope · GitHub

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# CITATION.cff — machine-readable citation metadata.
# https://citation-file-format.github.io
#
# If you use STIMscope in your research, please cite BOTH the software
# (this repository) and the preferred-citation below.

cff-version: 1.2.0
title: "STIMscope"
message: "If you use this software, please cite both the software (this repository) and the preferred-citation."
type: software
authors:
  - given-names: "Hamid"
    family-names: "Chorsi"
    affiliation: "UCLA Department of Neurology / Department of Electrical and Computer Engineering"
  - given-names: "Saray"
    family-names: "Soldado-Magraner"
    affiliation: "UCLA Department of Neurobiology"
  - given-names: "Yan"
    family-names: "Jin"
    affiliation: "UCLA Department of Neurology"
  - given-names: "Imaan"
    family-names: "Soltanalipouryekesammak"
    affiliation: "UCLA Department of Electrical and Computer Engineering"
  - given-names: "Alex"
    family-names: "Zheng"
    affiliation: "UCLA Department of Computer Science"
  - given-names: "Dejan"
    family-names: "Markovic"
    affiliation: "UCLA Department of Electrical and Computer Engineering"
  - given-names: "Daniel H."
    family-names: "Geschwind"
    affiliation: "UCLA Department of Neurology"
  - given-names: "Peyman"
    family-names: "Golshani"
    affiliation: "UCLA Department of Neurology"
  - given-names: "Dean V."
    family-names: "Buonomano"
    affiliation: "UCLA Department of Neurobiology"
  - given-names: "Daniel"
    family-names: "Aharoni"
    affiliation: "UCLA Department of Neurology"
license: "GPL-3.0"
repository-code: "https://github.com/Aharoni-Lab/STIMscope"
url: "https://github.com/Aharoni-Lab/STIMscope"
abstract: >
  Spatio-Temporal 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 (DMD) for patterned illumination, and a GPU-based processing
  unit coordinated by a microcontroller for hardware-level
  synchronization. Distributed as a Docker image for NVIDIA Jetson
  alongside the accompanying CRISPI software pipeline.

preferred-citation:
  type: article
  title: "STIMscope: centimeter-scale all-optical imaging and patterned optogenetic manipulation at single-cell resolution"
  authors:
    - given-names: "Hamid"
      family-names: "Chorsi"
      affiliation: "UCLA Department of Neurology / Department of Electrical and Computer Engineering"
    - given-names: "Saray"
      family-names: "Soldado-Magraner"
      affiliation: "UCLA Department of Neurobiology"
    - given-names: "Yan"
      family-names: "Jin"
      affiliation: "UCLA Department of Neurology"
    - given-names: "Imaan"
      family-names: "Soltanalipouryekesammak"
      affiliation: "UCLA Department of Electrical and Computer Engineering"
    - given-names: "Alex"
      family-names: "Zheng"
      affiliation: "UCLA Department of Computer Science"
    - given-names: "Dejan"
      family-names: "Markovic"
      affiliation: "UCLA Department of Electrical and Computer Engineering"
    - given-names: "Daniel H."
      family-names: "Geschwind"
      affiliation: "UCLA Department of Neurology"
    - given-names: "Peyman"
      family-names: "Golshani"
      affiliation: "UCLA Department of Neurology"
    - given-names: "Dean V."
      family-names: "Buonomano"
      affiliation: "UCLA Department of Neurobiology"
    - given-names: "Daniel"
      family-names: "Aharoni"
      affiliation: "UCLA Department of Neurology"
  year: 2026
  journal: "bioRxiv"
  doi: "10.64898/2026.05.27.728160"
  url: "https://www.biorxiv.org/content/10.64898/2026.05.27.728160v1"
  license: "CC-BY-NC-ND-4.0"

# Hardware + standards the platform depends on.
references:
  # DMD controller wire protocol.
  - type: report
    title: "DLPC3479 Software Programmer's Guide (DLPU081A)"
    authors:
      - name: "Texas Instruments"
    institution:
      name: "Texas Instruments"
    notes: >
      Wire-level I²C protocol for the TI DLP4710 DMD with the DLPC3479
      controller used by the projector engine.

  # Industrial camera SDK.
  - type: software
    title: "IDS Peak SDK"
    authors:
      - name: "IDS Imaging Development Systems GmbH"
    url: "https://en.ids-imaging.com/download-peak.html"
    notes: >
      USB3 industrial camera SDK (GenICam node map) used for hardware
      camera acquisition in the validated configuration.

  # Camera transport / node-map standard.
  - type: standard
    title: "GenICam — Generic Interface for Cameras"
    authors:
      - name: "European Machine Vision Association (EMVA)"
    notes: >
      Standard behind the camera trigger / node-map abstraction
      surfaced in the GUI's Sensor Settings dialog.