Identifying channels present in czi generated from Zeiss

Hi All,

I am looking at a dataset generated from Zeiss microscope. In the dataset description, it is mentioned

3 stain (MsGcg,RbCol4,SMACy3) confocal images of the pancreas for microvasculature analysis

The immunofluorescence studies were completed to identify the microvasculature of the pancreas by examining images for stained alpha-cells, smooth muscle cells and basement membrane.

I’m not able to understand which stain (MsGcg,RbCol4,SMACy3) corresponds to alpha-cells, smooth muscle cells and basement membrane. Also how can we identify which channel

Input file is available here in > primary/Controls-Vascstain/sub-6368/sub-6368_20x_MsGcg_RbCol4_SMACy3_islet1.czi.

import napari
import napari_aicsimageio
from aicsimageio import AICSImage
from aicsimageio.writers import OmeTiffWriter

img = AICSImage(‘sub-6368_20x_MsGcg_RbCol4_SMACy3_islet1.czi’)
img.data # returns 6D STCZYX numpy array
print(img.dims) # returns string “STCZYX”
print(img.shape) # returns tuple of dimension sizes in STCZYX order

first_channel_data = img.get_image_data(“ZYX”, C=1, S=0, T=0)

with OmeTiffWriter(“file.ome.tiff”) as writer:
writer.save(
first_channel_data,
pixels_physical_size=img.get_physical_pixel_size(),
dimension_order=“ZYX”,
)

channel_names = img.get_channel_names()

Output of channel ids:
[‘Ch2 M-T1’, ‘Ch1-T2’, ‘Ch3-T2’]

I am not sure which channel corresponds to what (alpha-cells, smooth muscle cells and basement membrane). For instance, if I want to reconstruct a 3D volume using this dataset which channel has to be used.

Any help will be highly appreciated.

I am a beginner in this field, kindly excuse me for the naive questions.

Hi,

based on my python script I get the info below. So you did get the channel names correctly but the actual dye names might be of interest as well.

Since you use AICSImageio (with pylibCZI) the 6D array has the shape: (1, 1, 3, 48, 1024, 1024) - [STCZYX], which means to get separate Z-Stacks for every channel would be something like:

  • array[0, 0, 0, :, :, :] = Alexa Fluor 488 = Ch2 M-T1
  • array[0, 0, 1, :, :, :] = Alexa Fluor 405 = Ch1-T2
  • array[0, 0, 2, :, :, :] = Cy3 = Ch3 T2
Directory	C:\Users\m1srh\Downloads
Filename	sub-6368_20x_MsGcg_RbCol4_SMACy3_islet1.czi
Extension	czi
ImageType	czi
SizeX	1024
SizeY	1024
SizeZ	48
SizeC	3
SizeT	1
SizeS	1
SizeB	1
SizeM	1
isRGB	False
ObjNA	0.8
ObjMag	20
ObjID	Objective:0
ObjName	None
ObjImmersion	Air
XScale	0.415133
YScale	0.415133
ZScale	1
XScaleUnit	None
YScaleUnit	None
ZScaleUnit	None
DetectorModel	[None, None, None]
DetectorName	[None, None, None]
DetectorID	[Detector:0:0, Detector:1:0, Detector:1:1]
DetectorType	[PMT, PMT, PMT]
InstrumentID	[]
Channels	[Alexa Fluor 488, Alexa Fluor 405, Cy3]
ChannelNames	[Ch2 M-T1, Ch1-T2, Ch3-T2]
ImageIDs	[]
NumPy.dtype	uint16
Axes_czifile	BVCTZYX0
Shape_czifile	(1, 1, 3, 1, 48, 1024, 1024, 1)
Axes_aics	STCZYX
Shape_aics	(1, 1, 3, 48, 1024, 1024)
SizeX_aics	1024
SizeY_aics	1024
SizeC_aics	3
SizeZ_aics	1
SizeT_aics	1
SizeS_aics	1
dims_aicspylibczi	{'X': (0, 1024), 'Y': (0, 1024), 'Z': (0, 48), 'C': (0, 3), 'T': (0, 1), 'V': (0, 1), 'B': (0, 1)}
dimorder_aicspylibczi	BVTCZYX
size_aicspylibczi	(1, 1, 1, 3, 48, 1024, 1024)
czi_ismosaic	False
PixelType	Gray16
SizeH	1
SizeI	1
SizeV	1
SW-Name	AIMApplication
SW-Version	14.0.0.201
1 Like

@sebi06

Could you please let me know how to obtain the information posted below these lines ?

Also, did you mean to say
Alexa Fluor 488 = Ch2 M-T1 #green-fluorescent dye
Alexa Fluor 405 = Ch1-T2 # blue-fluorescent dye
Cy3 = Ch3-T2 # orange-fluorescent dye

I’m still not able to understand which stain (Alexa Fluor 488,Alexa Fluor 405,Cy3 ) corresponds to alpha-cells, smooth muscle cells and basement membrane.

Yes, sorry for the typos. I corrected my post. This is what the metadata say.