HOW TO USE OUR SERVICE

The Alpinus Spectra service (hereinafter referred to as the Service) is intended for loading, storing, modifying and processing spectral data, including comparing spectra with similarity assessment, for creating, saving and using PLSR, PLSR-DA models.

Information: The Service is in testing mode, therefore changes in functions and interface are possible that are not described in the manual. For additional information, you can use the feedback form.

To gain access to the main functions of the Service, it is enough to authorize via a Google account. The authorization button is in the upper right corner of the working window. After authorization, access to the "My Spectra" and "My Models" workspaces appears. Without authorization, access is only possible to several data sets for the purpose of testing the main functions of the Service. Access without authorization does not provide the ability to load spectra and save models in the database.

The Service is in testing mode, therefore the number of spectra that can be loaded after authorization and the number of models that can be stored are limited. The maximum number of spectra is 250 (both for comparison and for models - predictor matrix or X-block), the maximum number of Y-vectors (response vectors) is 50, the maximum number of PLSR models is 5, the maximum number of PLSR-DA models is 5.

If you click the authorization button again after authorization, you will get access to general information about your spectra (1), to the feedback form (2), which contains fields for:

1. Entering a current contact e-mail (by default, the e-mail from the Google account);
2. Entering information;
3. Attaching a screenshot or other image.

By clicking the button (3), an email with the attached information will be sent to our service department.

At the bottom of the form there is a log out button (4).

This page is only available after authorization. It provides access to your private information - spectra for the comparison and search module, X data matrix and Y-block for modeling, subtypes for spectrum classification, etc. You can download, change and delete any of your information.

Information: all your data is stored in encrypted form, so even in case of unauthorized access to the database, we maintain the privacy and integrity of your data.

The page is divided into a download block (1-6) and a block of available data (7):

When loading a spectrum (1), it is possible not only to select a file with data in *.csv format, but also to enter information about the spectrum (Spectrum Description) and information about the scan mode (Scan Parameters). This information will be saved in the database and linked to the data set. The choice of data type (2) affects the interface - if "Compare" is selected, then to load the spectrum you need to add a subtype (3). For PLSR, PLSR-DA models, the subtype is not selected. If there is information about which device was used to obtain the spectrum, then it can be selected in the list of devices (Choose Device). If there is no such information, then you can select the "no data" option. If the required device is not in the list, then you should contact the administrator with a request to add this device to the list. By default, all data in the database is stored on the "nm" scale. If the scale in the file has the "cm^-1" format, then this format must be specified (4). When loading the file, the conversion to nanometers will occur.

If the spectrum is saved to the database successfully, a corresponding message will appear in the modal window. If a failure occurs during saving, or the data file is damaged, the information will not be written to the database, and the message will contain information about the error.

When loading the Y-vector (5), it is possible to add a description of the information contained in the file (Data Description).

If there is a need to add a new subtype, then you should use the function (6) - loading data about a new subtype. You need to enter the name of the subtype and, if necessary, a description of the subtype. A subtype created by a user is available only to that user. Each user can have his own subtypes, but the main data types are added by the Service administration.

In block (7) there is information about all the data uploaded by the user and about all the subtypes created by the user. Some data fields can be changed; any data and subtypes can be deleted. Attention! - when deleting a subtype, the data associated with this subtype will automatically be permanently deleted. The data in the table can be sorted.

All spectra are downloaded as a *.csv file (square matrix). The first column of the file should contain sample names or numbers; the first row should contain the wavelength. An example of such a spectrum is shown in the following figure (1). If the spectrum matrix contains empty cells, cells with non-numeric values, various artifacts, then such a spectrum will either not be downloaded (you will receive an error message during download) or various errors will occur during processing of such a spectrum. The spectrum matrix should contain from one record to 10,000. If the number of records (samples) is significant (a thousand or more), then the processing speed slows down and the results of processing, searching, modeling should be expected for some time (up to several minutes). Data vectors (Y-block, response vector, reference values) should also be uploaded as a *.csv file. Currently, the Service supports only data vectors, i.e. one spectrum corresponds to one reference value. The appearance of such a file is shown in the following figure (2):

To pre-process spectra, use the "Spectra Visualizer" page. Page view with processed spectrum:

To select spectrum(s) for preprocessing, use the list of available spectra (1). The list (1) has a search function. After selecting the spectrum(s) for preprocessing, select the sequence of actions using the constructor (2). The constructor window view:

In the "Choose method" list, select the desired processing method. The "Add" button adds the method to the preprocessing sequence described in the "Methods string". When the processing sequence is formed, click the "Send" button to transfer it to the main program. The "Close" button closes the constructor window without transferring the preprocessing sequence.

Alternatively, if you have been using our service for a long time and remember the preprocessing encoding or preprocessing sequences saved in text format, you can enter them directly into the "Input processing chain" text field (4) without using the constructor.

Preprocessing is implemented by pressing the "Process" button. The result of the sequence execution is displayed in the image (8). The primary spectrum is displayed in the image (7).

Alternatively, if you have been using our service for a long time and remember the preprocessing coding or preprocessing sequences saved in text format, you can enter them directly into the "Input processing chain" text field (4) without using the constructor.

The implementation of preprocessing is carried out by pressing the "Process" button. The result of the sequence execution is displayed in the image (8). The primary spectrum is displayed in the image (7).

The data shown in figures (7) and (8) can be saved in the *.csv table format. To do this, use the "Download CSV" button (5).

If you use the Baseline Correction function (code - baselineals), the appearance of the baseline, which is subtracted from the spectrum(s), can be activated/deactivated with the "Show baseline" switch (6).