Open Specy
Authors: Win Cowger and Zacharias Steinmetz
Abstract: Open Specy provides commercial-grade FTIR and Raman spectroscopy analysis resources to the open-source community by allowing users to view, share, process, and identify FTIR and Raman spectra.
Full Description: Development:
Open Specy started from our lab’s need to have access to spectral analysis software (which can cost > $10k). In just the past year, Open Specy has grown into a global community of users and an ecosystem of functionality with advanced online and desktop functionality. Open Specy is a Shiny application embedded within a package (on CRAN and Github), which can call all of the basic functionality of the graphical user interface as functions to automate and extend analysis routines. Thanks to config files and some careful coding, we can push the app to shinyapps.io from the package and provide unique functionality for logging and data sharing on the online version (via mongodb and dropbox) while seamlessly using the same code for desktop deployment with run_app() where data can be shared to desktop folders and logs stored using the loggit package.
Use:
To get started using the app, users can upload spectra files in various formats or download the sample spectra we provide. Next, users can preprocess their spectra using baseline subtraction and smoothing techniques to amplify their signal-to-noise ratio. Lastly, users can identify their spectra using an onboard spectral library.
We have built-in accessibility features like language translation and colorblind-friendly graphics because accessibility is important to us. Most buttons in the app support descriptive popups on hover, and we have a detailed standard operating procedure. We also created a detailed video tutorial for new users.
Future:
The long-term vision for Open Specy is to completely reimagine the way we analyze Raman and IR spectra by developing artificial intelligence routines based on community-contributed data and code. We envision a future where anyone with a Raman or FTIR spectra in hand can accurately identify what it is without being a professional spectroscopist.
Keywords: Raman, FTIR, Spectroscopy, Open, Data, Community, hyperSpec, OpenSpecy, plotly, dplyr, hexView
Shiny app: https://wincowger.shinyapps.io/OpenSpecy/
Repo: GitHub - wincowgerDEV/OpenSpecy-package: Analyze, Process, Identify, and Share, Raman and (FT)IR Spectra
RStudio Cloud: Posit Cloud
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