Open TinaAngerer opened 3 years ago
AlanRace
commented
3 years ago Interesting, I don't think I have seen data exported from Image Quest before. That's definitely an error, the window shouldn't look like that. It seems it has somehow failed to initialise the default parameters for Interpolation Rebinning.
Did a console window (black background, white text) open too when you opened MATLAB? If so, could you please provide the error that is listed there?
TinaAngerer
commented
3 years ago Hi,
No (black BG, white text) console window is popping up. ATM I run the standalone version with MATLAB_Runtime_R2020a_Update_5_win64 but we would like to get a MATLAB licence next year.
May I ask, what version of MATLAB we would need, and do we need additional toolboxes or is the basic version enough?
Thnak you, -Tina
AlanRace
commented
3 years ago Hello, Okay, that certainly makes it a little trickier to debug. Is there any chance that you would be able to send the dataset (or any dataset that causes this issue) so that I can replicate it?
Most versions of MATLAB should work - I haven't tested yet with 2020b, but don't see any breaking changes in the release notes. The base version of MATLAB should be sufficient for most functionality (we tried to limit the use of toolboxes where possible), but for some of the statistics and machine learning methods (e.g. PCA, NMF, t-SNE) you may need the Statistics and Machine Learning Toolbox.
TinaAngerer
commented
3 years ago No problem, all my test datasets are on METASPACE and can now be downloaded (fyi same is true for everyone elses public datasets in case you need something to play with) https://metaspace2020.eu/datasets?q=Tina%20angerer
the one I used specificly is this one (20201007_Brain_Cer_DAN70_pos_i):
https://metaspace2020.eu/annotations?ds=2020-10-07_14h37m17s&q=dan70
And i just noticed something. When I look at the individual pixel spectra, some of them start at m/z 0, some of them at 500 (I recorded mass range 400-2000). I tried the Zero filling on a pixel spectrum that started at 400 --> no problem:
spectrum starts at 0 --> problem:
As for why some pixel spectra would start at 0, that I don't know.
We are very intested in the statistical functions, so we'll have to invest in this one.
Thank you, -Tina
Describe the bug If I want to perform the zero filling function, the window that pops up does not contain all the buttons. see picture. it`s independent of which zero filling option I choose.
To Reproduce Steps to reproduce the behavior:
Expected behavior I don't know what it should look like, but apparently I'm missing an 'OK' button
Screenshots If applicable, add screenshots to help explain your problem.
Software version
If using source code, MATLAB version (please complete the following information):
Desktop (please complete the following information):
Additional context The file I want to analyze is an imzml file, converted from a raw-file using image quest (MALDI-Orbitrap image).