RamApp, a modern hyperspectral imaging toolbox for processing and analysis

An intuitive and user-friendly web application to explore Raman maps

Features

Main Features

RamApp is a web application that aims to provide a user-friendly solution allowing researchers from various backgrounds to easily and successfully explore hyperspectral data, with a focus on Raman imaging

Interoperability

Import data obtained from different sources, including the most diffused commercial software

Pre-processing

RamApp covers the most-used tools and techniques for Raman maps: from cropping and smoothing to spikes detection and baseline correction

Map analysis

Analyse Raman maps using statistical data analysis methods such as clustering, PCA, multivariate curve resolution (MCR) and N-FINDR

Stacked images composition

Create, as individual or stacked images, intensity maps with a high level of customization

Export

Export publication-quality images or raw data for further analysis

User-friendly design

Interactively explore and visualise the data and the results of each processing step with a fast and easy work environment

Personal storage

Once uploaded, your data will be stored in a safe and personal space

Cloud-based solution

Access the app from any browser and operating system without requiring a local installation

Stay updated

News & events

Aug 31, 2023

RamApp at ICAVS12

RamApp was recently presented at the 12th International Conference on Advanced Vibrational Spectroscopy.

Jun 24, 2022

RamApp at SPEC 2022

We were thrilled to attend a conference in Dublin to show our most recent app development.

Partners

Project developers

Our Team

Meet The Team

Here are the main people who contributed to the development of RamApp.

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Renzo Vanna
Senior Researcher @ CNR-IFN
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Giulia De Poli
Data scientist @ Datrix
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Andrea Masella
Data scientist @ Datrix
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Elia Broggio
Data scientist @ Datrix
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Dario Polli
Associate Professor @ Polimi
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Matteo Bregonzio
CTO @ Datrix
Credits

Citing RamApp

We are currently in the process of writing a paper that will detail the development and functionality of our application. In the meanwhile, you can directly cite our website as a reference.

Citations

Publications

Vernuccio, F., Broggio, E., Sorrentino, S., Bresci, A., Junjuri, R., Ventura, M., Vanna, R., Bocklitz, T., Bregonzio, M., Cerullo, G., Rigneault, H., & Polli, D. (2024). Non-resonant background removal in broadband CARS microscopy using deep-learning algorithms. Scientific Reports, 14(1). 10.1038/s41598-024-74912-5

Junjuri, R., Calvarese, M., Vafaeinezhad, M., Vernuccio, F., Ventura, M., Meyer-Zedler, T., Gavazzoni, B., Polli, D., Vanna, R., Bongarzone, I., Ghislanzoni, S., Negro, M., Popp, J., & Bocklitz, T. (2024). Estimation of biological variance in coherent Raman microscopy data of two cell lines using chemometrics. The Analyst. 10.1039/d4an00648h

Bresci, A., Kobayashi-Kirschvink, K. J., Cerullo, G., Vanna, R., So, P. T. C., Polli, D., & Kang, J. W. (2024). Label-free morpho-molecular phenotyping of living cancer cells by combined Raman spectroscopy and phase tomography. Communications Biology, 7(1). 10.1038/s42003-024-06496-9

Antonacci, G., Vanna, R., Ventura, M., Schiavone, M. L., Sobacchi, C., Behrouzitabar, M., Polli, D., Manzoni, C., & Cerullo, G. (2024). Birefringence-induced phase delay enables Brillouin mechanical imaging in turbid media. Nature Communications, 15(1). 10.1038/s41467-024-49419-2

Vanna, R., Masella, A., Bazzarelli, M., Ronchi, P., Lenferink, A., Tresoldi, C., Morasso, C., Bedoni, M., Cerullo, G., Polli, D., Ciceri, F., De Poli, G., Bregonzio, M., & Otto, C. (2024). High-resolution Raman imaging of >300 cells from human patients affected by nine different leukemia subtypes: a global clustering approach. Analytical Chemistry, 96(23), 9468–9477. 10.1021/acs.analchem.4c00787

Karlo, J., Gupta, A., & Singh, S. P. (2024). In situ monitoring of the Shikimate pathway: A combinatorial approach of Raman reverse stable isotope probing and hyperspectral imaging. The Analyst, 149(10), 2833–2841. 10.1039/d4an00203b

Vernuccio, F., Vanna, R., Ceconello, C., Bresci, A., Manetti, F., Sorrentino, S., Ghislanzoni, S., Lambertucci, F., Motiño, O., Martins, I., Kroemer, G., Bongarzone, I., Cerullo, G., & Polli, D. (2023). Full-Spectrum CARS Microscopy of Cells and Tissues with Ultrashort White-Light Continuum Pulses. The Journal of Physical Chemistry. B, 127(21), 4733–4745. 10.1021/acs.jpcb.3c01443

Ardini, B., Bassi, A., Candeo, A., Genco, A., Trovatello, C., Liu, F., Zhu, X., Valentini, G., Cerullo, G., Vanna, R., & Manzoni, C. (2023). High-throughput multimodal wide-field Fourier-transform Raman microscope. Optica, OPTICA, 10(6), 663. 10.1364/OPTICA.488860

Ghislanzoni, S., Kang, J. W., Bresci, A., Masella, A., Kobayashi-Kirschvink, K. J., Polli, D., Bongarzone, I., & So, P. T. C. (2023). Optical Diffraction Tomography and Raman Confocal Microscopy for the Investigation of Vacuoles Associated with Cancer Senescent Engulfing Cells. Biosensors, 13(11), 973. 10.3390/bios13110973

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FAQ

Any Questions? Answered

Don't hesitate to contact us if you have more questions

At the moment, RamApp can accept files from Renishaw™ grid map (*.wdf), Horiba™ LabSpec 5 (*.ngc), CSV tables (*.csv), Apache Parquet/Feather (*.parquet/*.feather), MATLAB™/Octave ( *.mat) and also custom-defined formats. We plan to extend the compatibility with other file formats in the next months according to the users needs.
Yes, you can export the processed hyperspectral cube as CSV tables (*.csv), Feather data frames (*.feather) or MATLAB™/Octave file (*.mat). In addition, you can export the entire RamApp project (*.zarr) which also includes the generated images and masks.
Currently RamApp is only available as an online web application because we believe that this approach has some advantages. For example it can be accessed from any platform, making it independent from the operative system. It is also easier to distribute and maintain: updates and bug fixes can be made easily and quickly, without the need for users to download and install anything.
As of today RamApp is supported by EU projects funds. In the future, we will consider alternative solutions such as donations or premium features to keep the project alive, but the current functionalities will always remain free for everyone.
The following features are already present on RamApp: map rotation, spatial and spectral crop, spatial and spectral smooth (denoising), cosmic rays detection and removal (despike), data resampling using a new spectral grid with equally-spaced nodes (helps to compare data having different calibration axes), data normalization, baseline correction, optical substrate identification and removal, cluster analysis, principal component analysis (PCA), multivariate curve resolution (MCR) and N-FINDR.
RamApp acts solely as a data processor, and the property of any uploaded data remains with you. If you choose to cancel the data from your personal space, we will promptly erase it from our servers. For further details, please refer to our Terms & Conditions (clause 8.4).

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Start exploring the potential of RamApp now.

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