Msi data table export

msi-data-table-export

Summary

Export mean intensity spectra and region-of-interest (ROI) derived m/z vs. intensity tables from MSI-Explorer as CSV or HDF5 files for downstream biochemical annotation and statistical analysis. This skill bridges napari-based MSI visualization and external analytical workflows.

When to use

After calculating mean intensity values across all spectra in an MSI dataset (or within a manually selected ROI), and you need to store the resulting m/z–intensity table in a portable format for downstream ROI analysis, database annotation, or external statistical pipelines.

When NOT to use

• If you need to export raw spectral data without aggregation (use data import/visualization export instead).
• If your MSI data is still in profile mode and has not been converted to centroid mode, as mean calculation requires discrete m/z bins.
• If you require real-time streaming of spectra during ongoing data acquisition rather than batch export of computed results.

Inputs

• napari MSI layer with loaded imzML or vendor-specific mass spectrometry imaging data
• calculated mean intensity spectrum (array of m/z and intensity pairs)
• optional: user-drawn ROI mask (label layer)

Outputs

• CSV file containing m/z vs. mean intensity table
• HDF5 file containing m/z vs. mean intensity table with metadata
• PNG export of spectrum plot (optional)

How to apply

Following mean spectrum calculation in MSI-Explorer (via 'Show true mean spectrum'), click 'Export spectrum data' to serialize the plotted m/z vs. intensity table as a CSV file; alternatively, select the HDF5 format for compatibility with complex hierarchical metadata. For ROI-specific exports, first define the ROI using the brush and label tools, calculate the ROI mean spectrum via 'Calculate ROI mean spectrum', then export. The exported table contains columns for m/z values and their corresponding arithmetic mean intensities; verify row count matches the number of unique m/z values detected across the dataset.

Related tools

• napari (Plugin host and visualization framework for interactive MSI layer display and ROI selection prior to export) — https://github.com/napari/napari
• MSI-Explorer (napari plugin that implements mean intensity calculation, ROI workflow, and CSV/HDF5 export functionality) — https://github.com/MMV-Lab/MSI-Explorer
• Python (Runtime environment for MSI-Explorer and CSV/HDF5 I/O libraries (csv, h5py))

Evaluation signals

• Exported CSV/HDF5 file exists and is readable by standard data analysis tools (pandas, R data.frame).
• Row count in exported table equals the number of unique m/z values detected across all spectra in the dataset.
• Column headers are present and labeled 'm/z' and 'mean_intensity' (or equivalent); no missing or NaN values in m/z column.
• For ROI exports: row count is less than or equal to the full dataset table; intensity values are non-negative and within expected range for the normalization method applied.
• File timestamp and size are consistent with the scale of the input MSI dataset (e.g., 1000–100,000 m/z bins × 4–8 bytes per value).

Limitations

• Export does not include uncertainty/variance estimates for individual m/z mean intensities; only point estimates are stored.
• CSV export is human-readable but lacks schema metadata; HDF5 is recommended for large datasets or when provenance tracking is critical.
• ROI export requires manual selection via napari brush; automated ROI definition is not supported by this export skill alone.
• Export inherits all preprocessing applied before mean calculation (noise reduction, normalization, hotspot removal); no option to export raw vs. processed side-by-side in a single file.

Evidence

• [other] For each unique m/z value across all spectra, calculate the arithmetic mean of intensities at that m/z across all pixels/samples. Aggregate results into a structured table (m/z vs. mean intensity) and save as a CSV or HDF5 file compatible with downstream ROI analysis and annotation workflows.: "Aggregate results into a structured table (m/z vs. mean intensity) and save as a CSV or HDF5 file compatible with downstream ROI analysis and annotation workflows."
• [readme] To export the plotted data as .csv file, click Export spectrum data. To save the spectrum plot as image, click Export spectrum plot.: "To export the plotted data as .csv file, click Export spectrum data."
• [readme] To select the ROI, click on Select ROI for mean spectrum. Adjust the brush size and label color. You can fill the area by using paint icon. Then click on the Calculate ROI mean spectrum. You can export as .csv file by using Export spectrum data.: "Then click on the Calculate ROI mean spectrum. You can export as .csv file by using Export spectrum data."
• [intro] It covers data import, visualization, mean intensity calculation, region of interest (ROI) analysis, annotation with selected databases and pre-processing such as noise reduction and normalization.: "It covers data import, visualization, mean intensity calculation, region of interest (ROI) analysis, annotation with selected databases and pre-processing such as noise reduction and normalization."