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Example: An imaging mass spec dataset was collected from 150-1000 m/z.
Usage: A ion image <150 m/z is extracted such as 70 m/z.
Problem: Instead of a blank image or error, an ion image for 150 m/z is extracted and reported.
Code example:
from pyimzml.ImzMLParser import ImzMLParser
from pyimzml.ImzMLParser import getionimage
f = ImzMLParser('file_path')
tol_ppm = mz * 3 / 1000000
x = getionimage(f, 70, tol=tol_ppm, z=1, reduce_func=sum)
x = hotspot_fill_2(x, 0.99)
plt.imshow(x, cmap='viridis', interpolation ='nearest')
plt.savefig('path', bbox_inches='tight')
The text was updated successfully, but these errors were encountered:
Example: An imaging mass spec dataset was collected from 150-1000 m/z.
Usage: A ion image <150 m/z is extracted such as 70 m/z.
Problem: Instead of a blank image or error, an ion image for 150 m/z is extracted and reported.
Code example:
from pyimzml.ImzMLParser import ImzMLParser
from pyimzml.ImzMLParser import getionimage
f = ImzMLParser('file_path')
tol_ppm = mz * 3 / 1000000
x = getionimage(f, 70, tol=tol_ppm, z=1, reduce_func=sum)
x = hotspot_fill_2(x, 0.99)
plt.imshow(x, cmap='viridis', interpolation ='nearest')
plt.savefig('path', bbox_inches='tight')
The text was updated successfully, but these errors were encountered: