---
# System prepended metadata

title: Agenda 2023-10-12
tags: [meeting, update]

---

# Agenda 2023-10-12

###### tags: `meeting` `update`
- Attendees
    - [x] Adam
    - [x] Alan
    - [x] Andy
    - [ ] Chi-Li
    - [x] Eric
    - [x] Micah
    - [x] Nathan
    - [ ] Nenad
- Previous Action Items


- Topics
    - CZI Make-a-thon updates
        - higher dimensional Zarr output
            - currently output TCYX (where C are channels on the camera sensor)
            - some needs (e.g. at biohub) to output TCZYX (where C may not be channels on the camera sensor - e.g. different optical filter, and Z might correspond to stage position)
            - are there similar needs at the allen institute?
            - is TCZYX enough? is acquisition in that order? or is there a need for more flexibility?
        - event trigger test bed
    - ROS2 exploration update
    - Spinnaker
        - Up in running in BioHub lab
        - BioHub team wants to use Micromanager-Acquire
    - Micah update?


- Meeting Minutes
    - CZI Make-a-thon week
        - Shalin's lab has a microscope w/ stage and change optical filter (polarization) => 4-5D Zarr (2 channels, time, z-stack)
        - current Zarr has TCZYX but does not account for Z; Andy wrote rough update to current implementation to account for Z
            - rewrote it to roll on Z instead of T
        - current implementation for TCZYX writes X>Y>Z>C>T; do we output to a completely different Zarr storage devices?
    - Adam's team does not run experiments w/ time component; there exists a performance consideration for T
        - current implementation maintains chunking over specific ROI over Y, X; perfomance impacted if/when trying to chunk across all dimensions
        - Adam's team would chunk across X, Y, Z
        - currently append to Z dimension, and chunk equally across X, Y
        - currently 128 x 128 when in cloud, want to go smaller but there is a penalty for going smaller
        - color is kept in a separate dimension
    - **Adam's team would still find this useful to be able to separate Z, C, T**
- event trigger test bed
    - Nathan programming a microcontroller to trigger
        - replacing a niDAQ w/ a $20 part that can be integrated into CI/CD to test triggering
- ROS2 exploration
    - Alan shows demo
        - device discovery and streaming
        - combine processes and coordinate via launch files (instead of running)
            - Stream & viewer spun up at same time
    - spun up multiple Acquire processes and viewers at the same time
        - use different name spaces
        - has client-host capabilities (run on PC and view on laptop) 
    - visualize in napari
        - hasn't yet coordinated w/ launch file but it's possible
    - our exploration is focused on the coordinated system
        - what are the deployment issues we'd run it?
- Micah update
    - been wrapping up on schema work and refactoring setup for diSPIM


- Action Items
  