Package: czi-shader
CZI Shader中文EnglishIntroductionThis 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.Installationpipinstallczi-shaderUsageExample:importcv2fromczi_shaderimportCZIChannel,shading_czip='/mnt/inner-data/sc-C057-146-O4213.czi'[print(c)forcinCZIChannel.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',illuminationtype='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:fromczi_shaderimportCZIMetap='/data/sdf/sc-C057-146-O4213.czi'meta=CZIMeta.from_czi(p)print('resolution:',meta.resolution)print('channels:')forchinmeta.channels:print(ch)output: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)