Add hyperspectral SWIR image analysis

[wincowgerDEV]

@afalty and I just spoke about their hyperspectral image analysis routine and database. They have plans to make the database and analysis routine open source and want to see it applied in Open Specy. I think this new technology has a ton of applications in microplastic research and overlap with other hyperspectral images for FTIR and Raman which we have plans to implement in the future.

Their database has 4 polymers, marine samples, PE, PET, PS, PP, weathered plastic, 250 particles of each polymer, Hyspex images, down to 100 microns - 150 microns, dry samples on a filter, preprocessing for light source.

They have a multivariate model to divide the particles by polymer type, Simca model, pca for each class.

They will share some preliminary code and data in the next month and will be publishing their results with a draft sent out by the new year, 3-4 months for publication.

Steps to implement the data and code:

• Add the reference dataset to Open Specy's file download list.
• Add a button on the home screen which allows the user to select that they want to analyze hyperspectral swir.
• Incorporate image upload and reshaping.
• Test file size limitations and set the upload limits so that Open Specy doesn't break.
• Incorporate image preprocessing.
• Incorporate the model classification.
• Incorporate the processed image visualization and reporting of particle sizes, shapes, and polymer types for the images.
• Develop new functions to implement in the CRAN package.

[Shreyas-Patankar]

very cool! @afalty we've had some success with PCA for dimensional reduction of hyperspectral images (repo Ocean-Wise/hyperspectral_tile_processing) but we don't have our own reference database - relying on OpenSpecy instead :D

our version of PCA does have limitations though (dealing with overlaps etc.) so would love to share notes!

[afalty]

Hey Shreyas, would love to hear about what you're working with. Feel free to drop me an email :) andrea.faltynkova@ntnu.no

[Shreyas-Patankar]

@afalty just sent you a note! also I'll be talking about this at the SETAC conference this month if you happen to be participating

[wincowgerDEV]

Interestingly just found this new R package to analyze maps that we might be able to build off of: https://www.researchgate.net/publication/355955630_uFTIR_An_R_package_to_process_hyperspectral_images_of_environmental_samples_captured_with_m_FTIR_microscopes

[zsteinmetz]

Great! Let me know if I can help.

[afalty]

Also just a quick correction, I unfortunately don't have nearly that much data for each polymer... I have varying numbers for each polymer type. I can say that the database I've accumulated is made up of 4770 spectra. This is more or less "ready" and I can send it along as a .csv or another format if you like. Only question is if you'd like it unprocessed or pre-processed. The way I see it the bare minimum would be correction for the light source.

[wincowgerDEV]

Hey Andrea, That would be really helpful! Unprocessed spectra would be best if you can share that, we can do the most with it. Warm Regards, Win

…

On Mon, Nov 8, 2021 at 7:33 AM Andrea Faltynkova ***@***.***> wrote: Also just a quick correction, I unfortunately don't have nearly that much data for each polymer... I have varying numbers for each polymer type. I can say that the database I've accumulated is made up of 4770 spectra. This is more or less "ready" and I can send it along as a .csv or another format if you like. Only question is if you'd like it unprocessed or pre-processed. The way I see it the bare minimum would be correction for the light source. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#105 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGMUJUY4UZBJYRGOHCCRJD3UK7UUHANCNFSM5HJL6EVA> . 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>.

-- ´¯`·.¸¸.·´¯`·.´¯`·.¸¸.·´¯`ツ ------------------------------ --------------------- *Win Cowger, PhD * Pronouns: he/him Research Scientist Moore Institute for Plastic Pollution Research *Contact Info* 515-298-3869 | ***@***.*** | @Win_OpenData <https://twitter.com/Win_OpenData> *Websites* Personal Website: www.wincowger.com Currently Employed: https://mooreplasticresearch.org/ Alumni Of: https://www.thegraylab.org/ Project Websites: www.openspecy.org Research Gate: https://www.researchgate.net/profile/Win-Cowger Github: https://github.com/wincowgerDEV OSF: https://osf.io/kxeh5/ ------------------------------------------------------------------------------------