neuralib.scanner

Confocal Scanner

  • This module provide the reading and parsing the Zeiss confocal dataset,

currently support .lsm & .czi format.

  • Use for batch processing/analysis, or other api integration.

(i.e., batch cell segmentation, manually stitching…)

  • For general image visualization, Zen/Fiji/ImageJ are recommended

Image Data Dim

Dimension parameters (DimCode):

V - view

H - phase

I - illumination

S - scene

R - rotation

T - time

C - channel

Z - z plane (height)

M - mosaic tile, mosaic images only

Y - image height

X - image width

A - samples, BGR/RGB images only

LSM format

from neuralib.scanner import LSMConfocalScanner

filepath = ...
lsm = LSMConfocalScanner.load(filepath)

# get the meta
print(lsm.meta)

# get the images array
print(lsm.lsmfile)

# zproj imshow
lsm.imshow(channel=2, zproj_type='max')

CZI format

from neuralib.scanner import LSMConfocalScanner

filepath = ...
czi = CziConfocalScanner.load(filepath)

# get meta
print(czi.meta)

# get dim code
print(czi.get_dim_code())

# get the image array
print(czi.get_image(channel=0, scene=1))

# zproj imshow
lsm.imshow()

Modules: