Mass spectrometry imaging and complementary techniques open collaboration.

Aims

• Bring MSI and image analysis experts together
• Collect and publish set of “benchmark” multi-modal data
• Design and develop new format/extension of imzML for multi-modal data
• Evaluate and compare existing registration methods on “benchmark” data

How can I get involved?

• Join us at the next meeting!
• Join one of the mailing lists to be kept up to date as the project progresses.
• Participate in one of the open discussions.
• Share your data to ensure your specific use-case is represented.
• Help us design a new data format for multi-modal data (data format mailing list).

Next meeting

The next meeting will take place on 16th December at 15:00 CET. For information on what has been discussed at previous meetings, please see the meeting notes.

Mailing lists

• MSI and co. project mailing list Subscribe
• Data format design/development mailing list Subscribe

Open discussions

• Quantifiable metrics for image registration accuracy
• Bridging the gap between MSI data and other fields

Sharing data

Data shared as part of this collaboration will help to:

• form a set of 'benchmark' data which will be published and hosted on a public data repository, similar in style to Oetjen et al., but focussed on multi-modal data.
• understand use-cases to develop new format/extension of imzML optimised for multi-modal data.
• evaluate existing image registration methods.
• design and develop new image registration and data integration methods.

If you decide to share data with this collaboration, you decide how your data will be used and how you would like to be acknowledged.

How to submit

Please provide the answers to the following questions in an email to us. We will set up a project folder for you and provide you with detailed instructions on how to upload your dataset.

1. Briefly describe the data, sample and scientific question in your own words.
2. Which MSI modality was used (MALDI, DESI, SIMS,...)?
3. What pixel size was used (μm)?
4. Which secondary modality was used?
5. What pixel size was used (μm)? Note: If you are uploading raw microscopy data, this is typically included in the metadata and so can be omitted.
6. If more than two modalities were acquired, please include answers to 4. and 5. for the remaining modalities.
7. What registration accuracy would enable you to answer your research question?
8. Who can be contacted regarding the data (name, institute, email)?
9. Would you like the opportunity to present your data/challenge at a subsequent meeting?
10. Which purpose(s) are you willing for your data to be used (e.g. inclusion in benchmark dataset, development of new algorithms, development of new format)?
11. If your data forms part of the benchmark dataset, which licence would you like to use (e.g. CC BY 4.0, CC0 1.0)?
12. How would you like to be acknowledged (e.g. acknowledgement section, citation, Zenodo DOI, authorship) if your data is used in a publication prior to its release as part of the benchmark dataset?

Acknowledgements

This project was supported by a virtual mobility grant from the COST action COMULIS CA17121.