MITI (minimum information guidelines for highly multiplexed tissue images)
A set of technologies combining imaging with sequencing technology has now become known under the term „spatial omics“. With appropriate setups, it is possible to resolve, for example, gene expression profiles of many genes not only at the level of single cells (single-cell RNA sequencing) but also at the level of single cells in the original tissue context (i.e., with the spatial information of where the transcripts are located in the tissue; spatial transcriptomics). Different technical solutions exist for this task. One approach is highly multiplexed tissue imaging in which a prepared tissue section is imaged multiple times in a row, each time staining for another target mRNA (the staining of which can be washed out after each run). For example, specific nucleotide probes coupled to fluorophores can be used to quantify the RNA amplicons in situ (in the tissue) based on the fluorescence signal intensity in the microscopy image.
The MITI guidelines are structured in “levels” that cover metadata items like biospecimen, reagent, data acquisition, and data analysis. Metadata levels for imaging with antibodies, aptamers, peptides, dyes, and similar detection reagents are considered (Shapiro et al., 2022). The guidelines describe the data at five data levels:
- Level 1 refers to raw image tiles in original file formats
- Level 2 is assembled data into multi-channel images or image sets
- Level 3 describes a dataset after quality control and potentially with segmentation masks or similar
- Level 4 data contains spatial feature tables used for analysis with dimensionality reduction (e.g. UMAP) or similar.
- Level 5 would be the top level of integrated spatial features with images.
To enable researchers to collect all the metadata items, the authors provide standardized collection formats in the supplementary material (e.g., a spreadsheet format entry mask). These tools allow to pick metadata items from pre-defined entries. The entries are then validated by the tool.
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