Write tutorial for registration of MALDI and histology images

[kostrykin]

There is a workflow for registration of mass spectrometry image data (MALDI) and histology images: https://usegalaxy.eu/published/workflow?id=64bb7a64877034dc This interdisciplinary analysis serves the combined quantification of MALDI and histological microscopy images.

However, there might be a newer version of the workflow, maybe even on IWC! Melanie Föll mentioned, that she was considering submitting a revised version.

And there is also a paper about it: Föll et al., GigaScience 2019

Given the paper, writing the tutorial should be kind of straight-forward.

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Things to be done:

• Check whether we have data suitable for this workflow? Preferably, use the data from the paper.
• Determine which version of the workflow is best suited for a tutorial? This would probably be the one on IWC, if there is one by now. It might be helpful to talk to Melanie Föll.
• Write the tutorial which covers the reproduction and usage of the workflow.

[sklumpe]

I am currently trying to reproduce this workflow. Will keep you posted on how far I get with it.

[sklumpe]

We ran into the following problem trying to import data in imzML format that we could not resolve. The datatype is defined here (to be the best of our knowledge):

https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/proteomics.py

The problem is that imzML files are recognized as mzml files and cannot be dragged/dropped into the preprocessing tab / MSI data field:

The manual overwrite in the edit--> datatype tab is not listing the imzML file format.

@bgruening

[kostrykin]

@sklumpe We just figured out during breakfast that IMZML is a composite data type, which logically consists of two files. To upload a composite file into Galaxy, you need to use the Upload data button and then there is a tab specifically dedicated to uploading composite data types. There you should be able to even select IMZML specifically, and then you will be asked for the two files.

[bgruening]

@foellmelanie is there a newer version of this workflow?

[bgruening]

Before you spend a lot of time on this, please try to put composite files into the job.yml description. For tools we need to need to do this: https://github.com/galaxyproteomics/tools-galaxyp/blob/b1b03bb7cd31c1ec806b286d6c9444428b358e15/tools/cardinal/colocalization.xml#L140

I hope this works in the job.yml files as well.

[foellmelanie]

Hi all,
sorry for the late reply, great that you are working on this.
There is a newer version of the workflow, however it is different in some aspects as it uses (automatically) generated annotations from QuPath software as input. So when using Gimp or Photoshop for annotation the workflow you are refering to is still up to date. However, we hardly use it anymore as our pathologists prefer to work with QuPath software and for this we have an adjusted/updated workflow. We also have a tutorial, which is just unfortunately not yet on GTN but only exists locally. What are your plans / aims for this topic?

[kostrykin]

Much thanks for the follow-up @foellmelanie

I think that for the purpose of a tutorial it is fine to have a tutorial that's not using the most recent version of the workflow, because it is more about instructing and teaching (and it could benefit from the lower complexity of not requiring QuPath).

However, we've been stuck because we don't have the input images for the workflow, so @sklumpe has been trying to reproduce those images from the raw data, but without luck yet. Any chance you could provide us the images?

[foellmelanie]

Here is the workflow including input data, I hope that helps, otherwise please let me know:
https://usegalaxy.eu/u/melanie-foell/h/bladder-msi-history1-tma1-co-registration