MITI: Minimum Information about Tissue Imaging

Minimum Information about Tissue Images (MITI) reporting guidelines comprise minimal metadata for highly multiplexed tissue images and were developed in consultation with methods developers, experts in imaging metadata (e.g., DICOM and OME) and multiple large-scale atlasing projects; they are guided by existing standards and accommodate most multiplexed imaging technologies and both centralized and distributed data storage.

The YAML files in this repository provide detailed specification of the standard, as outlined in [LINK TO PAPER]. Individual files capture attributes, their description and significance, but also additional information that is essential for validating specific files; this includes ensuring that data in each field has the correct data type and that it meets constraints on valid values. Each attribute is associated with one of the following data types:

• boolean, integer, float, string - Standard data types representing boolean, integer, floating-point and character strings
• filename - A valid POSIX-portable filename
• date - A date specified in the ISO 8601 standard YYYY-MM-DD
• doi - A valid DOI identifier
• rrid - A valid Research Resource Identifier

Valid values are specified as sets of predefined keywords for string and as [min, max] intervals for integer and float variables, where both min and max can be optionally omitted to define one-sided intervals.

Example 1

The following YAML block defines a required attribute Tumor tissue type that relates to collection and processing of biospecimens. A valid field must be specified as a character string, using one of the pre-defined keywords: Primary Tumor, Local Tumor Recurrence, etc.

Tumor tissue type:
  description: Text that describes the kind of disease present in the tumor specimen
    as related to a specific time point.
  category: Collection and Processing
  type: string
  valid-values:
  - Primary Tumor
  - Local Tumor Recurrence
  - Distant Tumor Recurrence
  - Metastatic
  - Premalignant
  significance: required

Example 2

The following YAML block defines a recommended attribute Cycle Number, which must be specified as a 1-based index (i.e., an integer belonging to the one-sided interval [1, Inf)).

Cycle Number:
  description: 'the cycle # in which the co-listed reagent(s) was(were) used'
  type: integer
  valid-values:
    min: 1.0
  significance: recommended