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Welcome to the improv wiki!

Module Documentations

Plan for organizing the repo:

data/: Symbolic links to synced folders (such as Dropbox) with large data files
doc/: Text-based documentation not already added into Python docstrings
src/: Top-level directory for all source code. Further divided into modules, e.g. src/visual/
test/: Top-level directory for all test code. Mirrors the src directory structure

Configure experimental setup:
- Choose image acquisition source, which chooses an Acquisition module
- Choose processing sources, currently only caiman. Can be broken out:
  - Motion correction
  - Neuron/component identification
  - Spike extraction
- Choose analysis sources to obtain inferences
- Configure other experimental parameters (size, rate, expected components, etc)
- Configure display options: either choose module, or configure default visualization
Initialize server:
- Load data store -- need to consider persistence between days and sessions
- Load chosen experimental parameters
- Initialize chosen pipeline components
Run server:
- Pipeline components wait or run depending on signals from nexus server
- Front end interfaces with the user and the server

Front end as GUI is run first
- Creates Nexus and communicates with it
- Nexus can alternatively be run as stand-alone on command line
- Has store client from Nexus from which to pull images, plots
- Also hands off user-input in the form of configuration to Nexus
Nexus runs inside front-end and handles all communication
- Starts data store server and handles clients interfacing with the store
- between front-end (user) and other components
- between components in the form of signaling
Other components: analysis, processing, etc
- Have access to the store through the client provided by Nexus