Weekly Summaries NeuroGears: NeuroThom

[NeuroThom]

📑 Weekly Consultancy Log – Neurogears @NeuroThom

This log contains links to weekly consultancy updates for Neurogears work at the lab. These start from 2025-12-05. Previous summaries from the Coen lab can be found here. This repo will eventually be deprecated in favor of using ucl-open repositories.

Each week’s entry summarises meetings, development work, debugging, and discussions.

[NeuroThom]

Weekly Update – Neurogears Consultancy (Week of 08-12-25)

🗂 Core Acquisition and Logging Infrastructure

• Worked extensively on the ucl-open/acquisition package, focusing on core operator and infrastructure development.
• Added and refined C# operators, including time-grouping utilities and software event generation.
• Improved logging behaviour, including updates to LogData to append to CSV by default and support for JSON-based logging.
• Fixed initialisation issues in the SerialDevice operator and aligned serial device handling across packages.

🧩 Schema and Rig Integration

• Developed and expanded ucl_open_rigs as a concrete schema and testing environment for shared rig definitions.
• Added autogenerated classes from Pydantic schemas and automated the schema-to-code generation pipeline.
• Integrated visual stimulation schemas to ensure compatibility across repositories, including a single co-authored change importing schema elements from hf_visual.
• Refactored device and display definitions, introducing screen abstractions and removing legacy calibration patterns.

🧪 Templates and Documentation

• Added usage instructions to the rig-template repository to support adoption of the Copier-based template for new rigs and experiments.

🧠 Context

• This week primarily involved independent implementation work, building on requirements and design decisions clarified through discussions in previous weeks.

⏱ Hours

• Monday (08-12-25): 10 hours
• Wednesday (10-12-25): 6 hours
• Friday (12-12-25): 1 hour
• Total: 17 hours

[NeuroThom]

Weekly Update – Neurogears Consultancy (Week of 18-12-25)

🗂 Shared Repositories

• Continued building out the shared ucl-open infrastructure across rig-template, acquisition, and new experimental repo for 2AFC task, av-dome.
• Focus this week was on integrating additional hardware components and tightening dependencies to support reproducible workflows.

🧪 Template and Dependency Updates

• Updated rig-template to improve the default development setup:
  • upgraded Spinnaker version
  • added a default Extensions.csproj for Bonsai.sgen output
  • bumped local development packages from ucl-open/acquisition
  • removed unnecessary dependencies (tensorflow, contraqtor, and default Aeon acquisition dependency)
  • added ucl-open-rigs dependency by default

⚙️ Acquisition Devices and Environment

• Extended ucl-open/acquisition with new devices and Bonsai support:
  • added TriggeredSpinnaker
  • added LicketySplitDevice
  • added ArduinoLedDriver
  • added RunningWheel controller for the BehaviorBoard
  • updated the Bonsai environment to support the new modules

🎛 AV Dome Hardware Integration

• Updated ucl-open/av-dome to use the open-ucl framework and added hardware extensions:
  • stepper motor extensions and hardware components aligned with rig and template updates
  • extension to control LEDs via SerialDevice - should move this to acquisition

⏱ Hours

• Development work: 12 hours
  • Thursday (18-12-25): 4 hours
  • Friday (19-12-25): 9 hours
• Meetings: 1 hour
• Total: 14 hours

[NeuroThom]

Weekly Update – Neurogears Consultancy (Week of 25-12-25)

NeuroGears was closed from 2025-12-21 til 2026-01-06

🗂 Shared Repositories

• Continued development work across ucl-open repositories, focused on integration, cleanup, and stabilisation rather than new feature development.

⚙️ Acquisition and Package Updates

• Updated the acquisition package to include shader support and aligned dependent package versions.
• Made small workflow adjustments to improve correctness and clarity, including changes to default behaviour and explanatory updates.

🎛 AV Dome (2AFC) Workflow

• Simplify wiring and workflow composition.
• Removed development extensions and updated Harp-related packages.
• Integrated locally built acquisition packages to ensure consistency during testing.

🧱 Rig Definitions and Devices

• Extended ucl_open_rigs with additional device definitions:
  • added LickSpoutStageDriver device
  • added stepper driver device type definitions
• Refactored LED controller class names for clarity
• Simplified BehaviorBoard-remove redundant descriptors.

⏱ Hours

• Sunday: 2hrs
• Tuesday: 5hrs
• Total: 7hrs

[NeuroThom]

Weekly Update – Neurogears Consultancy (Week of 01-01-26)

HAPPY NEW YEAR!

• No development activity recorded in the ucl-open repositories during this period.

⏱ Hours

• 0 hrs(holiday)

[NeuroThom]

Weekly Update – Neurogears Consultancy (Week of 08-01-26)

🗂 Shared Repositories

• Continued development across ucl-open core repositories, focusing on extending the acquisition stack, and migrating workflow to ucl-open/av-dome and using the newer packages and discriminators.

⚙️ Acquisition Operators and Video Support

• Extended ucl-open/acquisition with new operators and infrastructure:
  • added UclOpen.Video project and supporting operators/data classes for camera capture
  • added CreateRepository operator to support session metadata/versioning workflows
  • added operators for hardware communication, e.g. CreateDigitalOutputs and CreateStepperMessage operators for hardware control
  • added LickSpoutStage stepper driver device

🎛 AV Dome Workflow Updates

• Updated ucl-open/av-dome to align with the evolving ucl-open packages and schemas:
  • added Bonsai.Video
  • updated camera definitions to use the new discriminator approach
  • added tooling and scripts to generate classes from pydantic through the entire stack (and added Bonsai.Sgen as a local dotnet tool)
  • upgraded Harp and other ucl-open package dependencies

🧩 Schema and Device Model Refinement

• Refined ucl_open_rigs schemas and base classes to support the updated json/sgen pipeline:
  • refactored discriminator classes for the json/sgen stack
  • reduced SerialDeviceModule to only the required properties
  • added threshold properties to LicketySplit
  • recapitulated base classes rather than inheriting directly from Aeon

⏱ Hours

• Tuesday: 8 hours
• Friday: 2 hours
• Total: ~10 hours