Request help for pattern file creation

[BlakneyG]

I am trying to finish a pipeline that takes data collected on a combined Thermo Velos, Spectroglyph source, and Predator data station based acquisition into imzML. I am currently at the point where I have a Spectroglyph position file in XML and a mzML file from msconvert. I pulled the command list from the command line and that plus observation from other questions here, I have an idea about how to handle the syntax except for the -p command. Is there any guidance on how I can mimic an established file starting with an XML position file?

An outgoing research member left a small trial data set from a previous workflow. I will attach files from this test XML and an image to show the X-Y pattern that I hope to create. The actual images would of course contain many additional pixels. This work would provide a straight forward path for the users of the National FT-ICR MS User Facility to process their high resolution data imaging when combined with DataCubeExplorer and other imzML associated tools.

Thanks in advance,
Greg Blakney

pos3sPredatorSmall_positionFile.xml.txt

[AlanRace]

Hi Greg,
Sorry for the delay. The -p command expects a text file that is formatted like so (imzML expects coordinates to start at (1,1)):

1 1 1
2 1 1
3 1 1

where each line describes the coordinate (x, y, z) for scans in the mzML file in the order in which they appear. To skip a scan (if this is necessary) you can do (skipping the second scan:

1 1 1
-1 -1 -1
2 1 1

So I guess the quickest way to get up and running would be to write a script that parses the XML file and outputs a .txt file with the above format.

Perhaps a better (but longer term) solution would be to allow your XML file format as input in the -p command. I'm not sure whether this is something you (or your group) would be interested in contributing?

Alan

[BlakneyG]

Thanks for the information, this will get me up and running on the project. I will discuss with the group on the longer term solution once we get the immediate need covered. Also I want to make sure everything scales to several full size datasets and verify that this contrived learning set is indeed a valid test of the conversion method. The short term end goal for us is to most efficiently convert very large raw time domain datasets (100 GB and up) into a portable solution for users. Ideally we could convert directly to imzML without intermediate disk writes but my core is ANSI C (for speed) and I’ll need to look into some options to glue the code bits together. Some users / groups like Ron Heeren or Don Smith will happily process the data to meet their own needs, but we also get some folks that always use the stock vendor solution and come to us if they want 10 or 100X the resolving power. Thanks again, Greg From: Alan Race ***@***.***> Sent: Wednesday, September 22, 2021 8:02 AM To: AlanRace/imzMLConverter ***@***.***> Cc: BlakneyG ***@***.***>; Author ***@***.***> Subject: Re: [AlanRace/imzMLConverter] Request help for pattern file creation (#8) Hi Greg, Sorry for the delay. The -p command expects a text file that is formatted like so (imzML expects coordinates to start at (1,1)): 1 1 1 2 1 1 3 1 1 where each line describes the coordinate (x, y, z) for scans in the mzML file in the order in which they appear. To skip a scan (if this is necessary) you can do (skipping the second scan: 1 1 1 -1 -1 -1 2 1 1 So I guess the quickest way to get up and running would be to write a script that parses the XML file and outputs a .txt file with the above format. Perhaps a better (but longer term) solution would be to allow your XML file format as input in the -p command. I'm not sure whether this is something you (or your group) would be interested in contributing? Alan — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#8 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/APITMOHRG375FMIFX3URQJLUDHAUHANCNFSM5EAZDQ6Q> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub> .

[AlanRace]

Hi again, I am currently working on a new version/project that doesn't rely on Java (for exactly these kind of interoperability challenges) and that also goes directly from raw data to imzML (without the intermediate step). We've also had a lot of issues with file sizes around the 100 GB mark, hence starting this project. It's still in the early stages though. If you'd be willing to share some example data perhaps we can figure out a solution that works for both of our needs. Feel free to email me: race at uni-marburg dot de Thanks, Alan