# 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)