# 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