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.
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:
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.