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Mouse registration (Algorithm (Fluoro to Nissl, CTB to Nissl, Nissl to…
Mouse registration
Algorithm
Fluoro to Nissl
CTB to Nissl
Nissl to atlas
Pipeline
Limitations
QC of each step is via videos generated into dropbox
A step is interrupted in case of error in just one section of a series
multiprocessing is not available for transformation step
Results reside in user folders on bnb
Maintenance
Touch points are in web, integration scripts, algo scripts
Capabilities
Manual stepping of series through 5 steps
Execution
Progress
Dash board
Personnel for execution
Schedules
Data
Re-processing dataset
600+ AAV brains
400+ CTB brains
~20 AAVr brains
Freshly imaged brains
QC output to pipeline input is manual
LIMS could be queried for new brains which are QC passed
~10 per week
Feedback for issues and features
Tasks
version control
Documentation
Maintenance
New feature requests
Coronal vs transverse sections
Change of Atlas
Atlas-free steps
parameter tuning
code optimization
exception handling