Open wincowgerDEV opened 2 years ago
Shreyas-Patankar
commented
2 years ago 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
commented
2 years ago 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
commented
2 years ago @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
commented
2 years ago 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
commented
2 years ago Great! Let me know if I can help.
afalty
commented
2 years ago 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
commented
2 years ago 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.
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·.¸¸.·´¯·.´¯·.¸¸.·´¯ツ ------------------------------Win Cowger, PhD Pronouns: he/him Research Scientist Moore Institute for Plastic Pollution Research
Contact Info
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@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: