Data import/export

To import rectilinear or raw MSI data, or histopathology images, navigate to the Data tab.

Import MSI Data

1. Click ‘Select file…’ under MSI data. A file dialog box will open, allowing you to browse and select the file. MassVision supports different formats including:

   • Modality-independent structured MSI files (.csv)

   • Modality-independent hierarchical HDF5 files (.h5)

   • DESI MSI image files from Waters (.txt)

2. Select the format from the dropdown menu, select the file, and click ‘Open’ to load the data.

   Note

   The instruction on how to structure your MSI data into CSV or HDF5 compatible with MassVision can be found in Data Structure page.

3. After the data is loaded, general information like number of pixels, number of ions, and the name and location of the file will appears in the text box. The TIC visualization will also be displayed in the viewer. To adjust the image’s contrast, click the icon in the Slicer toolbar at the top of the screen. You can adjust the contrast by left-click-and-drag on the image or by selecting a region.

Import Reference Image

To load a gold-standard image like histopathology annotations, click ‘Select file…’ under Reference Image. A file dialog box will appear, allowing you to upload the desired image.

Raw MSI

MassVision can be used for processing and exploring raw MSI data in imzML format.

Import Data

Select file…

Click this button to load your raw imzML MSI data. After successful loading, the TIC (total ion current) image will appear in the view panel.

Data info

After loading a file, metadata will be displayed here, including spatial dimensions, number of spectra, m/z range, etc.

Spectrum Plot

Select spectra

Use this button to place a fiducial marker on the TIC view of the MSI data. You can interactively change its position with the mouse. Multiple fiducials can be placed to inspect spectra from multiple pixels.

Plot spectra

Displays spectra for all interactively selected points in a plot for inspection.

Ion Image Plot

ion m/z

Enter the central ion of interest to be plotted.

tolerance m/z

Define the mass tolerance window around the ion of interest.

heatmap

Choose the colormap for ion image visualization.

Plot ion image

Generates an ion intensity heatmap across the tissue/sample at the specified range.

Peak Picking

Calibration

If enabled, performs lock-mass calibration on each pixel spectrum using the m/z defined in Reference peak (e.g., 554.2615).

Smoothing

If enabled, applies smoothing to spectra to reduce noise. The degree of smoothing can be adjusted via Kernel bandwidth:

• Smaller = less smoothing (more detail preserved)

• Larger = more smoothing (reduces noise, but may blur peaks)

Spectral filtering

If enabled, restricts spectra to the user-defined m/z window specified in Start / End (e.g., 600–900).

Number of ions

Sets the maximum number of ions to extract. Peak picking is based on the summed abundance across all pixels.

m/z resolution

Sets the decimal precision of the m/z values. Example: ``3`` → 0.001 m/z resolution

Process

Executes all selected processing steps (calibration, smoothing, filtering) to produce a rectilinear (cubical) dataset with a unified m/z list across all pixels.