Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Issue when extracting m/z below experimentally acquired data... #19

Open
DinosaurInSpace opened this issue Apr 14, 2020 · 0 comments
Open
Assignees
Labels

Comments

@DinosaurInSpace
Copy link

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')

@intsco intsco self-assigned this Apr 15, 2020
@intsco intsco added the bug label Apr 15, 2020
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

No branches or pull requests

2 participants