autoROI is overly aggressive in imaging a big area

SWC-Advanced-Microscopy / BakingTray

Serial-section automated anatomy extension for ScanImage

https://bakingtray.mouse.vision/

GNU Lesser General Public License v3.0

11 stars 5 forks source link

autoROI is overly aggressive in imaging a big area #313

Closed raacampbell closed 3 years ago

raacampbell commented 4 years ago

e.g. sample SP_HMV_Rabies-D1-Tail-1 has a rawData footprint of 156 GB and a cropped stitched image size of 144 GB. So very little time was saved because it's obviously taking images that are too large when imaging the full brain. Things to consider:

[ ] Check if we can decrease the expansion parameter (settings.mainBin.expansionSize)? It's currently 700 microns.
[ ] Can we tweak the aggressive tile addition parameter?
[ ] When cropping write to disk reports that tell us how much space was saved and how much total padded extra was imaged.
[ ] Log to disk how often it added tile rows so we see if it's reasonable.

raacampbell commented 3 years ago

Stitchit now logs how well the autoROI worked, so we have some baseline data.

raacampbell commented 3 years ago

Will start by making slow changes to the settings:

settings.mainBin.expansionSize = 700 to 600
settings.clipper.edgeThreshMicrons = 250 to 350
settings.clipper.growROIbyMicrons = 500 to 450

See: e080b28b8f8cd1e698428ae5180a09d5bb168cf7

raacampbell commented 3 years ago

This is now all OK. Has been for some time. I don't recall how I fixed it. :-/