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AlanRace / SpectralAnalysis

Software for the analysis and interactive exploration of spectral imaging data
https://alanrace.github.io/SpectralAnalysis/
Apache License 2.0
29 stars 9 forks source link

Difficulty with Bruker FlexImaging Data Files #17

Closed EmilySekera closed 4 years ago

EmilySekera commented 4 years ago

Hello,

Adam asked me to reach out and post the issue I've been having when attempting to use your package.

I was recently attempting to utilize SpectralAnalysis for data I had obtained from an imaging run that was completed on a Bruker FT-ICR. I was able to manage to get some data loaded but unfortunately it has run across similar issues to that I had with MSiReader and have talked to Ken about. He had attempted utilizing imzML converter to remove empty scans with no luck. He also ran the data through the imzMLValidator with no errors output.

The file it loads is primarily blank black space with a small portion of the bottom right corner actually displaying my data. Due to the size of the file I assume that this is why the software has been unable to work for me and tends to freeze up.

If you would like me to send any data files or provide any further information, please let me know.

Best,

Emily

AlanRace commented 4 years ago

Hi Emily, This is due to the fact that Bruker data store 'absolute' pixel coordinates (in respect to the imagable area), rather than relative pixel coordinates. If you can send me the .imzML part I can 'fix' it for this file.

If you have more than one file, we'll need to come up with a more general solution.

Alan

EmilySekera commented 4 years ago

Hi again,

Unfortunately I do have multiple files that I am working with. Is this something that you think I may be able to fix myself with a bit of guidance? I can also reach out to Bruker and see if they have any solutions as well.

Thanks again!

Emily

AlanRace commented 4 years ago

Hi Emily, Sorry for the delay - would you be able to send me a link to the data? I'll implement a fix in the parser.

Thanks,

Alan

EmilySekera commented 4 years ago

Hi Alan,

Thanks for getting back to me. I have included a link to one of the smaller data files for you. I'm currently in the middle of moving but if you need any other files please let me know and I'll get it to you as soon as possible.

Best,

Emily 7dpi-section4.ibd https://drive.google.com/file/d/1WmcF4KlTgtvGuiBITt687851Q_VOF8g-/view?usp=drive_web 7dpi-section4.imzML https://drive.google.com/file/d/1Wix50xEUyP9N8MRx1kqopluntpnNWpVW/view?usp=drive_web

On Fri, Jun 5, 2020 at 9:09 AM Alan Race notifications@github.com wrote:

Hi Emily, Sorry for the delay - would you be able to send me a link to the data? I'll implement a fix in the parser.

Thanks,

Alan

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/AlanRace/SpectralAnalysis/issues/17#issuecomment-639469781, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAXUQES7XICZ5MKMFL4WR53RVDVBDANCNFSM4MPWVNLQ .

AlanRace commented 4 years ago

Hi Emily, I have now modified the underlying imzML parser to recognise when Bruker data is being read in and to automatically convert this to relative coordinate (rather than absolute) so that you can now visualise the data as expected.

Are you using the source code version? If so this is available in the lastest version 14b48bd

If not, I will make a new standalone version soon.

Thanks,

Alan

EmilySekera commented 4 years ago

Hi again,

I am using the source code version, I'll be sure to try it out this morning.

Thanks again for all of your help!

Best,

Emily

On Thu, Jul 9, 2020 at 8:09 AM Alan Race notifications@github.com wrote:

Hi Emily, I have now modified the underlying imzML parser to recognise when Bruker data is being read in and to automatically convert this to relative coordinate (rather than absolute) so that you can now visualise the data as expected.

Are you using the source code version? If so this is available in the lastest version 14b48bd https://github.com/AlanRace/SpectralAnalysis/commit/14b48bd61968cfa2abb65ca95568be6a24093389

If not, I will make a new standalone version soon.

Thanks,

Alan

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/AlanRace/SpectralAnalysis/issues/17#issuecomment-656089451, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAXUQETPCEXKMDFZPOWGZI3R2WXOZANCNFSM4MPWVNLQ .