# [27JUN22] Project plan

gantt  
 title 		Video acquisition controller with napari integration (H2 2022)
 dateFormat YYYY-MM-DD  
 axisFormat %Y %b
 excludes	weekends
 
 section napari streaming
 Start			 			:active, milestone, m1, 2022-07-01, 1d
 Nathan OOO                 :ooo1, after m1, 2w
 cpx-python stablization	:api1, after ooo1, 1w
  Research Engineer (Micah) start :crit, milestone, m2, 2022-08-01, 1d
 cpx-python to Adam/Micah         :crit, milestone, m2, 2022-08-01, 1d
 
 section Dual camera
 Develop and test           :dualcam1, after m2, 10d
 2 camera pipeline          :crit, milestone, m3, 2022-08-15, 1d
 
 section DAQ
 DAQ integration            :daq1, after m3, 10d
 Adam/Micah can adjust LightSheet live     :crit, milestone, m4, 2022-08-29, 1d
 
 section diSPIM
 Nathan 2nd visit          :visit1, after m4, 3d
 Integration and testing   :inttest1, after m4, 2w
 diSPIM operational        :crit, milestone, m5, 2022-09-30, 1d
 
 section Phase II microscope device support
 Stages                     :stage1, after m5, 10d
 metadata storage           :mstorage1, after stage1, 10d
 Downstream processing enabled :crit, milestone, m6, 2022-10-31, 1d
 
 section Support & Maintenance
 Integration support        :support1, after m6, 30d

 
 Section Production system
 1-2 brain routine scanning :crit, milestone, m7, 2022-11-15, 1d
 Thanksgiving Break         :ooo2, 2022-11-21, 5d
 Christmas Break            :ooo3, 2022-12-21, 2w

 section Wishlist items
 H5/Zarr streaming          :crit, milestone, 2023-03-15, 10d
 Laser engine                      :laser1, 2023-03-15, 10d
 Filter wheel               :fwheel1, 2023-03-15, 10d
 Vibratome                  :vibra1, 2023-03-15, 10d

## Narrative

In H1 we delivered proof-of-principle software capable of acquiring single-view 3D fluorescence images via stage-driven light-sheet scanning on a diSPIM chassis. Additionally, we developed a python api that could be used to stream live video into Napari for 30 Hz display.

The python API is an important part of delivering software that is essential to our partner, Adam Glaser. The instruments he develops are mainly controlled with python-based software. Our software will deliver a unique capability - performant dual-camera video streaming. Additionally,

Adam Glaser is developing microscopes with the aim of achieving a fully functional sample acquisition pipeline by the end of the year. That will require our software is highly reliable. Additionally, we will need to ensure the software can capture certain metadata critical for his downstream processing pipeline.

## Goals

This half the theme is to deliver a python api and additional device support so that Adam Glaser has *reliable* software that is an *essential* part of his acquisition pipeline.

### Non-goals

* "Wishlist items" are nice-to-have, but are not critical toward making the software essential. These are likely targets for future or contracted engineering effort not shown in this plan.

In the meantime, we TODO

Deliver a desktop application capable of acquiring high-speed video. Video should be written to disk at a sustained bandwidth of 2 GB/s. The application should expose services that allow communicating with a locally running napari instance. These services should provide a video stream for observing the acquisition and limited ability to configure and control the acquisition.

## Risks and Mitigations

* Nathan Clack as sole engineer
* Hiring
* Dependencies on Adam Glaser