neuralib.imaging.scanbox

ScanBox Data Parser

author:

Yu-Ting Wei

This module simply provides

  1. result parser for scanbox acquisition system

  2. view the sequence output

See all the info

from neuralib.imaging.scanbox import SBXInfo

file = ...  # scanbox .mat output file
sbx = SBXInfo.load(file)
print(sbx.asdict())  # print the information as dictionary

Save as Json

from neuralib.imaging.scanbox import sbx_to_json

file = ...  # scanbox .mat output file
output_file = ...  # *.json
sbx_to_json(file, outputfile)

Screen Shot file to tiff

from neuralib.imaging.scanbox import screenshot_to_tiff

file = ...  # scanbox .mat screenshot output file
output = ... # *.tiff
screenshot_to_tiff(file, output)

SBXViewer

directly view the image sequence as mmap

Use CLI

See help:

python -m neuralib.imaging.scanbox.viewer -h

Example playing the 100-200 frames:

python -m neuralib.imaging.scanbox.viewer -D <DIR> -P <OPTIC_PLANE> -C <PMT_CHANNEL> -F 100,200

Example save 100-200 Frames as tiff:

python -m neuralib.imaging.scanbox.viewer -D <DIR> -P <OPTIC_PLANE> -C <PMT_CHANNEL> -F 100,200 -O test.tiff

Use API call

from neuralib.imaging.scanbox.viewer import SBXViewer

directory  = ...  # directory contain the .sbx and .mat output from scanbox
sbx_viewer = SBXViewer(directory)

# play
sbx_viewer.play(slice(100,200), plane=0, channel=0)

# save as tiff
sbx_viewer.to_tiff(slice(100,200), plane=0, channel=0, output='test.tiff')

Modules: