## Basic Workflow

SpectrumImager is designed with a minimalistic concept—keeping the interface as simple as possible while still providing the full range of functionality. If you believe the workflow could be made even easier or more convenient, please share your feedback with us.

The basic workflow proceeds by pressing the buttons in the lower band of the tool, from left to right.

## Open Dataset

Click the Open button and choose the spectrum-image file you wish to process. SpectrumImager can open files in Gatan (EELS and EDX), Velox (EDX), PantaRhei (EELS), Bruker (EDX), and other formats. The list of supported formats is continuously expanding; consult our website for the most up-to-date information.

Open Through Menu

SpectrumImager can handle only one dataset at a time. If you wish to work with several datasets in parallel, start another instance of SpectrumImager.

Some EDX spectrum-images may appear too large after import, which slows down processing. By default, SpectrumImager suggests limiting the upper energy range if no useful peaks are present.

Clipping Energy on Import

Another common issue in EDX spectrum-images is high sparsity. In such cases, SpectrumImager may apply automatic binning during export to make subsequent processing more efficient.

Automatic Binning

If available, the original calibration is read during import. You can check it and modify if neccesary under Data → Calibrate.

You may also reduce your dataset to remove defective pixels or exclude specific energy ranges. Use Data → Cut to adjust width, height, or energy channels.

If the opened file consists of the metadata information, you can check it by under Show → Metadata. Depending on the format of an imported file, some records in the original metadata can not be read or interpreted.

The spectrum type (EDX or EELS) is normally detected automatically during import. If not, set it manually under Data → Spectra Type.

## Review Dataset

After loading a file, you can inspect it in several ways:

- View a selected energy slice or integrate several slices using the horizontal scroll bar in the upper-right corner of the tool. The second scroll bar below controls the number of integrated slices (i.e., the width of the energy window).
- At this stage, only scrolling the Original dataset is available. If the dataset includes complementary images (e.g., dark-field or bright-field), select the AD/BF images option to display them. The upper scroll bar then allows you to scroll through all available images, while the window-width bar is disabled. Complementary Images
- Brightness, contrast, and gamma can be adjusted using the vertical scroll bars on the right.
- You can save the currently displayed image as a JPEG at any time via File → Save Display.
- To inspect a specific area, select a rectangular or oval region by pressing or in the lower-right corner of the tool. The average spectrum of the selected area will be shown.

  Spectrum Picker

  Scrolling Spectrum

- You can also create a line plot of the data clicking the button.

  Line Plot

- To quickly check intensity, place the mouse over a point of interest and read the value displayed in:
- Finally, you may subtract a background from the displayed signal by clicking the button. Background Subtraction

## Using SpectrumImager as a Format Converter

SpectrumImager can import and export many spectrum-image formats. Even if you don’t use its analysis tools, you can use it as a format converter. Open a file via the Open button or File → Import, then save it in your desired format via File → Export.

SpectrumImager also supports conversion of 2D images and 1D spectra. Use Settings → Proceed → Import → Dimensions to choose the dataset dimensionality.

## Data Denoising

The next button in the lower band is Denoise. Click it and wait until the progress bar completes. Denoising is performed using the PCA procedure described in P. Potapov and A. Lubk, Advanced Structural and Chemical Imaging (2019) 5:4 and usually requires no user interaction.

Details of PCA

PCA Settings

After this step, you will have both the original dataset and its denoised copy. You can switch between them using a radio selector, and all viewing options apply to either dataset.

Additionally, you can navigate in the retrieved PCA latent space clicking and — an alternative and powerful way to explore your data.

Navigate in PCA Space

## Endmembers

Endmembers (Under development.)

## Elements

Elements (Under development.)

## Save

When finished, you may want to save your work.

Important: Clicking the Save button stores the data in SpectrumImager’s intrinsic temdm format, not in the original import format. The advantage is that when you reopen this file later, both the original and denoised datasets will be immediately available — no need to repeat prior operations.

If you want to save data in other formats, use File → Export. You may export the original, the denoised, or both datasets in the format of your choice. Remember that you can always save the currently displayed image as a JPEG via File → Save Display.

SpectrumImager Help – Index

# Topics Index

Select a topic below:

- Open Through Menu
- Clipping Energy on Import
- Automatic Binning
- Complementary Images
- Spectrum Picker
- Scrolling Spectrum
- Background Subtraction
- Line Plot
- Details of PCA
- PCA Settings
- Navigate in PCA Space
- Frame Appearance
- Troubleshooting