czi-shader 0.1.5

Reproduce the appearance of CZI files (coloring raw data) seen in Zeiss Zen software, and provide channel information extraction of CZI files

CZI Shader

中文 English

Introduction

This project aims to reproduce the appearance of CZI files (coloring raw data) found in Zeiss Zen software using Python and provides a simple CZI channel information parser.

Installation

pip install czi-shader

Usage

Example:

import cv2
from czi_shader import CZIChannel, shading_czi

p = '/mnt/inner-data/sc-C057-146-O4213.czi'
[print(c) for c in CZIChannel.from_czi(p)]

res = shading_czi(p, scale_factor=0.01)
cv2.imwrite(p + '.png', cv2.cvtColor(res, cv2.COLOR_RGB2BGR))

Output:

CZIChannel(id=0, name='Cy5', bit_count_range=16, pixel_type='Gray16', dye_name='Cy5', short_name='Cy5', illumination_type='Fluorescence', dye_max_emission=673, dye_max_excitation=650, dye_id='McNamara-Boswell-0774', dye_database_id='66071726-cbd4-4c41-b371-0a6eee4ae9c5', color='#FFFF0014', original_color='#FFFF0014', color_mode=None, palette_name=None, gamma=None, low=0.0059662775616083005, high=0.03865110246433204, is_selected=None)
CZIChannel(id=1, name='Cy3', bit_count_range=16, pixel_type='Gray16', dye_name='Cy3', short_name='Cy3', illumination type='Fluorescence', dye_max_emission=561, dye_max_excitation=548, dye_id='McNamara-Boswell-0615', dye_database_id='66071726-cbd4-4c41-b371-0a6eee4ae9c5', color='#FFFFAD00', original_color='#FFFFAD00', color_mode=None, palette_name=None, gamma=None, low=0.006240939955748837, high=0.13965056839856566, is_selected=None)
CZIChannel(id=2, name='EGFP', bit_count_range=16, pixel_type='Gray16', dye_name='EGFP', short_name='EGFP', illumination_type='Fluorescence', dye_max_emission=509, dye_max_excitation=488, dye_id='McNamara-Boswell-0828', dye_database_id='66071726-cbd4-4c41-b371-0a6eee4ae9c5', color='#FF00FF5B', original_color='#FF00FF5B', color_mode=None, palette_name=None, gamma=None, low=0.004196231021591516, high=0.1739833676661326, is_selected=None)
CZIChannel(id=3, name='DAPI', bit_count_range=16, pixel_type='Gray16', dye_name='DAPI', short_name='DAPI', illumination_type='Fluorescence', dye_max_emission=465, dye_max_excitation=353, dye_id='McNamara-Boswell-0434', dye_database_id='66071726-cbd4-4c41-b371-0a6eee4ae9c5', color='#FF00A0FF', original_color='#FF00A0FF', color_mode=None, palette_name=None, gamma=None, low=0.003936827649347677, high=0.15408560311284047, is_selected=None)

You can see that the four fluorescence channels (Cy5, Cy3, EGFP, DAPI) along with their corresponding wavelengths, depths, display colors, and display upper and lower limits are listed. The final merged image comparison is shown below:

The main color tone is related to what is displayed in Zen, with slight differences due to the 0.01 scale used in generating the image.

example 2:

Get the physical resolution of the lens:

from czi_shader import CZIMeta

p = '/mnt/inner-data/sc-C057-146-O4213.czi'
meta = CZIMeta.from_czi(p)
print('image:', meta.image_info)
print('resolution:', meta.resolution)

print('channels:')
for ch in meta.channels:
    print(ch)

output:

image: CZIImageInfo(acquisition_date_and_time=datetime.datetime(2020, 12, 1, 4, 45, 35, 982910, tzinfo=datetime.timezone.utc), size_c=4, component_bit_count=16, pixel_type='Gray16', size_x=71234, size_y=56688, size_s=1, size_m=839, original_compression_method='JpgXr', original_encoding_quality=85, acquisition_duration=1716335.2106)
resolution: CZIPhysicalResolution(x=<Quantity(6.5e-07, 'micrometer / pixel')>, y=<Quantity(6.5e-07, 'micrometer / pixel')>)
channels:
CZIChannel(id=0, name='Cy5', bit_count_range=16, pixel_type='Gray16', dye_name='Cy5', short_name='Cy5', illumination_type='Fluorescence', dye_max_emission=673, dye_max_excitation=650, dye_id='McNamara-Boswell-0774', dye_database_id='66071726-cbd4-4c41-b371-0a6eee4ae9c5', color='#FFFF0014', original_color='#FFFF0014', color_mode=None, palette_name=None, gamma=None, low=0.0059662775616083005, high=0.03865110246433204, is_selected=None)
CZIChannel(id=1, name='Cy3', bit_count_range=16, pixel_type='Gray16', dye_name='Cy3', short_name='Cy3', illumination_type='Fluorescence', dye_max_emission=561, dye_max_excitation=548, dye_id='McNamara-Boswell-0615', dye_database_id='66071726-cbd4-4c41-b371-0a6eee4ae9c5', color='#FFFFAD00', original_color='#FFFFAD00', color_mode=None, palette_name=None, gamma=None, low=0.006240939955748837, high=0.13965056839856566, is_selected=None)
CZIChannel(id=2, name='EGFP', bit_count_range=16, pixel_type='Gray16', dye_name='EGFP', short_name='EGFP', illumination_type='Fluorescence', dye_max_emission=509, dye_max_excitation=488, dye_id='McNamara-Boswell-0828', dye_database_id='66071726-cbd4-4c41-b371-0a6eee4ae9c5', color='#FF00FF5B', original_color='#FF00FF5B', color_mode=None, palette_name=None, gamma=None, low=0.004196231021591516, high=0.1739833676661326, is_selected=None)
CZIChannel(id=3, name='DAPI', bit_count_range=16, pixel_type='Gray16', dye_name='DAPI', short_name='DAPI', illumination_type='Fluorescence', dye_max_emission=465, dye_max_excitation=353, dye_id='McNamara-Boswell-0434', dye_database_id='66071726-cbd4-4c41-b371-0a6eee4ae9c5', color='#FF00A0FF', original_color='#FF00A0FF', color_mode=None, palette_name=None, gamma=None, low=0.003936827649347677, high=0.15408560311284047, is_selected=None)