metabolite-feature-organization
Summary
Organize spatial metabolomics mass spectrometry data into a structured AnnData object by parsing binary imzML files, extracting m/z values and intensity matrices, and mapping them to spatial coordinates. This skill is essential for downstream cross-modal spatial analysis in multi-omics workflows.
When to use
You have raw imzML and ibd (ion binary data) files from spatial mass spectrometry imaging and need to convert them into a standardized AnnData representation where m/z values are features (columns), spatial spots are observations (rows), and intensities form the feature matrix. Use this skill before alignment, normalization, or cross-modal integration with spatial transcriptomics data.
When NOT to use
- Input data is already in CSV or tabular format (use read_sm_csv_as_anndata instead)
- Mass spectrometry data is from a non-spatial experiment (imzML is specific to spatial imaging)
- AnnData object has already been constructed and validated
Inputs
- imzML file (text metadata file describing mass spectrometry imaging experiment)
- ibd file (ion binary data file containing mass spectrometry intensities)
Outputs
- AnnData object with intensity matrix in .X, m/z values in .var, spatial coordinates and spot IDs in .obs
How to apply
Load the imzML file and its accompanying ibd file using the spatialmeta.pp.read_sm_imzml_as_anndata function from the spatialMETA preprocessing module. This function parses mass spectrometry intensities and m/z values from the binary format, organizing them into a feature matrix with m/z as columns (variables) and spatial coordinates as rows (observations). Construct an AnnData object with the intensity matrix stored in the .X slot, m/z values in .var, spatial coordinates and spot identifiers in .obs, and return the formatted object for downstream metabolomic analysis. Verify that all spatial spots are represented, m/z values are numeric and monotonically ordered, and intensity values are non-negative.
Related tools
Examples
from spatialmeta.pp import read_sm_imzml_as_anndata; adata = read_sm_imzml_as_anndata(imzml_file='sample.imzML', ibd_file='sample.ibd')
Evaluation signals
- AnnData object .X contains non-negative intensity values with shape matching (n_spots, n_mz_features)
- m/z values in .var are numeric, unique, and properly ordered
- Spatial coordinates in .obs correspond exactly to imzML coordinate system (x, y pixel positions)
- No missing values (NaN) in intensity matrix or coordinate data
- Total m/z feature count matches the number of parsed ions in the ibd binary data
Limitations
- Requires both imzML and ibd files to be present and co-located; missing ibd file will cause read failure
- Binary format compatibility depends on imzML specification version and vendor implementation
- Large imzML files with very high mass resolution or large spatial imaging areas may require substantial memory
Evidence
- [other] Load the imzML file and its accompanying ibd (ion binary data) file using the read_sm_imzml_as_anndata function from spatialMETA preprocessing module.: "Load the imzML file and its accompanying ibd (ion binary data) file using the read_sm_imzml_as_anndata function from spatialMETA preprocessing module"
- [other] Parse mass spectrometry intensities and m/z values from the binary format, organizing them into a feature matrix with m/z as columns (variables) and spatial coordinates as rows (observations).: "Parse mass spectrometry intensities and m/z values from the binary format, organizing them into a feature matrix with m/z as columns (variables) and spatial coordinates as rows (observations)"
- [other] Construct an AnnData object with the intensity matrix in the .X slot, m/z values stored in .var, spatial coordinates and spot identifiers in .obs, and return the formatted object for downstream metabolomic analysis.: "Construct an AnnData object with the intensity matrix in the .X slot, m/z values stored in .var, spatial coordinates and spot identifiers in .obs, and return the formatted object for downstream"
- [readme] spatialMETA is a method for integrating spatial multi-omics data. SMOI aligns ST and SM to a unified resolution: "spatialMETA is a method for integrating spatial multi-omics data. SMOI aligns ST and SM to a unified resolution"
1---2name: metabolite-feature-organization3description: Use when you have raw imzML and ibd (ion binary data) files from spatial mass spectrometry imaging and need to convert them into a standardized AnnData representation where m/z values are features (columns), spatial spots are observations (rows), and intensities form the feature matrix.4license: CC-BY-4.05---67# metabolite-feature-organization89## Summary1011Organize spatial metabolomics mass spectrometry data into a structured AnnData object by parsing binary imzML files, extracting m/z values and intensity matrices, and mapping them to spatial coordinates. This skill is essential for downstream cross-modal spatial analysis in multi-omics workflows.1213## When to use1415You have raw imzML and ibd (ion binary data) files from spatial mass spectrometry imaging and need to convert them into a standardized AnnData representation where m/z values are features (columns), spatial spots are observations (rows), and intensities form the feature matrix. Use this skill before alignment, normalization, or cross-modal integration with spatial transcriptomics data.1617## When NOT to use1819- Input data is already in CSV or tabular format (use read_sm_csv_as_anndata instead)20- Mass spectrometry data is from a non-spatial experiment (imzML is specific to spatial imaging)21- AnnData object has already been constructed and validated2223## Inputs2425- imzML file (text metadata file describing mass spectrometry imaging experiment)26- ibd file (ion binary data file containing mass spectrometry intensities)2728## Outputs2930- AnnData object with intensity matrix in .X, m/z values in .var, spatial coordinates and spot IDs in .obs3132## How to apply3334Load the imzML file and its accompanying ibd file using the spatialmeta.pp.read_sm_imzml_as_anndata function from the spatialMETA preprocessing module. This function parses mass spectrometry intensities and m/z values from the binary format, organizing them into a feature matrix with m/z as columns (variables) and spatial coordinates as rows (observations). Construct an AnnData object with the intensity matrix stored in the .X slot, m/z values in .var, spatial coordinates and spot identifiers in .obs, and return the formatted object for downstream metabolomic analysis. Verify that all spatial spots are represented, m/z values are numeric and monotonically ordered, and intensity values are non-negative.3536## Related tools3738- **spatialMETA** (Provides the read_sm_imzml_as_anndata preprocessing function that parses imzML/ibd files and constructs AnnData objects) — https://github.com/WanluLiuLab/SpatialMETA3940## Examples4142```43from spatialmeta.pp import read_sm_imzml_as_anndata; adata = read_sm_imzml_as_anndata(imzml_file='sample.imzML', ibd_file='sample.ibd')44```4546## Evaluation signals4748- AnnData object .X contains non-negative intensity values with shape matching (n_spots, n_mz_features)49- m/z values in .var are numeric, unique, and properly ordered50- Spatial coordinates in .obs correspond exactly to imzML coordinate system (x, y pixel positions)51- No missing values (NaN) in intensity matrix or coordinate data52- Total m/z feature count matches the number of parsed ions in the ibd binary data5354## Limitations5556- Requires both imzML and ibd files to be present and co-located; missing ibd file will cause read failure57- Binary format compatibility depends on imzML specification version and vendor implementation58- Large imzML files with very high mass resolution or large spatial imaging areas may require substantial memory5960## Evidence6162- [other] Load the imzML file and its accompanying ibd (ion binary data) file using the read_sm_imzml_as_anndata function from spatialMETA preprocessing module.: "Load the imzML file and its accompanying ibd (ion binary data) file using the read_sm_imzml_as_anndata function from spatialMETA preprocessing module"63- [other] Parse mass spectrometry intensities and m/z values from the binary format, organizing them into a feature matrix with m/z as columns (variables) and spatial coordinates as rows (observations).: "Parse mass spectrometry intensities and m/z values from the binary format, organizing them into a feature matrix with m/z as columns (variables) and spatial coordinates as rows (observations)"64- [other] Construct an AnnData object with the intensity matrix in the .X slot, m/z values stored in .var, spatial coordinates and spot identifiers in .obs, and return the formatted object for downstream metabolomic analysis.: "Construct an AnnData object with the intensity matrix in the .X slot, m/z values stored in .var, spatial coordinates and spot identifiers in .obs, and return the formatted object for downstream"65- [readme] spatialMETA is a method for integrating spatial multi-omics data. SMOI aligns ST and SM to a unified resolution: "spatialMETA is a method for integrating spatial multi-omics data. SMOI aligns ST and SM to a unified resolution"
HolobiomicsLab