---
# System prepended metadata

title: '2022-02-03'
tags: [meeting, update]

---

# 2022-02-03 

###### tags: `meeting` `update`
[last meeting](https://hackmd.io/pc5dcFoVRgiOKl_ynj5BRg)

## Agenda
 * [Adam] Requirements
 * [Nathan] Notes from Ivan/Cameron meeting (https://hackmd.io/2n74xTPqRsuO-3_HjIMChw)
 * [Justine] Contractor SOW

## Requirements

1. DATA ACQUISITION
* REQUIRED
   * Operating 2x cameras (simultaneously)
      * 1.9 GB/sec (950 MB/sec/camera)
      * Sustained over tiles of up to 500 GB/camera (1 TB total)
      * Downtime of only 5-10 seconds between tiles (20 tiles total)
      * Downtime of ~5 minutes between slices (up to 20 slices total)
      * Reliable metadata tracking
 * PREFERRED
      * Some form of online compression -> reduces network requirements to storage server
      * Online writing of multi-resolution pyramid -> facilitates real-time monitoring of scan quality
      * Saved with BDV specification -> enables immediate ingestion into existing stitching tool(s), i.e. BigStitcher
2. GRAPHICAL USER INTERFACE
   * REQUIRED
      * GUI button to toggle live display of cameras ON/OFF
      * Overlaid display -> facilitates evaluation/alignment of dual-views
      * Adjust camera ROI (rows and columns)
      * Adjust camera exposure time
      * GUI tab to control 2x ‘light-sheet generators’ with real-time adjustment -> expedites alignment for each specimen
      * Light-sheet center position (x galvo DC offset)
      * Light-sheet width (x galvo amplitude)
      * Light-sheet planar focusing (y galvo adjustment DC offset)
      * Light-sheet rotation (y galvo amplitude)
      * Light-sheet digital scanning frequency (x/y galvo frequencies)
      * Light-sheet axial position (tunable lens adjustment)
      * Light-sheet scanning delay time (syncing with camera rolling shutter)
      * Camera slit width (syncing with light sheet)
      * GUI tab to set experiment parameters
      * Data location (drive, directory)
      * Volumetric scanning bounds
      * Tiling widths (lateral, vertical)
      * Spacing between frames along tile
      * Channels (laser powers per channel)
   * OPTIONAL
      * Channels acquired sequentially (scan same tile repeatedly changing filters)
      * Channels interleaved (scan tile once, interleaving with multi-band filter)


- Acquisition dimensions
    - software timed
        - slices (vibratome cuts)
        - tiles  (long stage addressed image strips)
        - channels (change filters, reset stage pos for tile)
    - hardware timed
        - z (hardware timed, stage master) 4500
        - xy (hardware timed, camera acq) 2304x2304

### Storage

Downstream 
- 5 GB/s to 500 TB Vast 
    - tested on linux NFS
- to HPC for lossy compression
- to cloud
    - big stitcher
    - segmentation/neuron tracing
    - collaborative proof-reading in AWS cloud-based janelia workstation

Acquisition File Format
- BigDataViewer+hdf5
    - each file contains an xyz stack for a particular tile and channel
    - internal chunking desirable for compression
    - bdv xml + files in a directory tree
    - (Does ImarisWriter fit requirements)

### Hardware

- Timing
    - Master clock is per frame
        - supplied by PCIe-6738 (or stages?)
    - Triggers
        - acquisition start (volume/stack)
        - frame start
        - (all stage/master driven)
    - AO (6 ch)
        - finite, per-frame
        - triggered on frame start
        - control (6ch):
            - 2x 1ch tunable lens
            - 2x 2ch mems mirror
    - DO (6-8 ch)
        - 4-6ch laser engine
        - 2x 1ch frame triggers to camera
            - relayed from daq
    - AI (?)
        - mirror feedback? (prob no)
        - laser intensity feedback? (no)
        - (other?)
    - DI
        - frame trigger
            - generated by stage controller
              (encoder sync output mode)
              
Other forms of feedback:
- view images as being acquired
- autofocus w some gui assistance during setup

#### Devices:

- Hamamatsu ORCA-Fusion BT camera
    - SDK https://dcam-api.com/dcam-sdk-login/
    - Active Silicon Frame Grabber (AS-FBD-4XCXP6-2PE8)
https://dcam-api.com/assets/pdfs/AS-FBD-4XCXP6-2PE8-Hamamatsu.pdf
    - 4x CoaXPress (CP-6 links)
    - 6.25 Gbps each (25 Gbps max)
    - 8-lane Gen2 PCI Express interface
    (linux but not public, requires signed agreement)
- Oxxius L6cc laser engine
    - RS232 (Serial)
- MS8000 stage (ASI)
    - RS232 (Serial) http://www.asiimaging.com/docs/products/serial_commands
- ASI light-sheet generator (MEMs mirror + tunable lens)
    - Drive with analog voltages (NI card)
- Leica VT1200S vibratome
    - Janelia (jET) microcontroller (RS232)
- NI DAQ (PCIe 6738)
    - 16-bit resolution
    - 32 analog output voltage channels (-10, +10V)
    - 8 digital I/O 5V TTL lines
    - 2x 24-bit, 20 MHz counters/timers
    - 1 MS/sec update rate (up to 8 outputs)
    - 350 kS/sec (>8 outputs)
    - 10 ns timing resolution
    - C++ SDK (https://www.ni.com/en-us/support/downloads/software-products/download.c-c---development-tools.html)

