Imaging Mass Spectrometry (IMS)

MIBI

Related files:

📝 Excel template: For metadata entry.
📝 TSV template: Alternative for metadata entry.

This schema is for Multiplex Ion Beam Imaging (MIBI). For MIBI, the channel_id (in the Antibodies TSV) is the name of the metal tag on the corresponding antibody. The other fields function the same way for all assays using antibodies. For more information, see the Antibodies TSV documentation.

Metadata schema

Version 1 (use this one)

Shared by all types

version
description
donor_id
tissue_id
execution_datetime
protocols_io_doi
operator
operator_email
pi
pi_email
assay_category
assay_type
analyte_class
is_targeted
acquisition_instrument_vendor
acquisition_instrument_model

Unique to this type

number_of_antibodies
number_of_channels
resolution_x_value
resolution_x_unit
resolution_y_value
resolution_y_unit
max_x_width_value
max_x_width_unit
max_y_height_value
max_y_height_unit
roi_description
roi_id
acquisition_id
area_normalized_ion_dose_unit
area_normalized_ion_dose_value
data_precision_bytes
dual_count_start
end_datetime
pixel_dwell_time_value
pixel_dwell_time_unit
pixel_size_x_value
pixel_size_x_unit
pixel_size_y_value
pixel_size_y_unit
preparation_instrument_vendor
preparation_instrument_model
primary_ion
primary_ion_current_value
primary_ion_current_unit
reagent_prep_protocols_io_doi
section_prep_protocols_io_doi
segment_data_format
signal_type
start_datetime
antibodies_path
contributors_path
data_path

Shared by all types

`version`

Version of the schema to use when validating this metadata.

constraint	value
enum	`1`
required	`True`

`description`

Free-text description of this assay.

constraint	value
required	`True`

`donor_id`

HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123.

constraint	value
pattern (regular expression)	`[A-Z]+[0-9]+`
required	`True`

`tissue_id`

HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456.

constraint	value
pattern (regular expression)	`(([A-Z]+[0-9]+)-[A-Z]{2}\d(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d(-\d+)+(_\d+)?)*`
required	`True`

`execution_datetime`

Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros.

constraint	value
type	`datetime`
format	`%Y-%m-%d %H:%M`
required	`True`

`protocols_io_doi`

DOI for protocols.io referring to the protocol for this assay.

constraint	value
required	`True`
pattern (regular expression)	`10\.17504/.*`
url	prefix: `https://dx.doi.org/`

`operator`

Name of the person responsible for executing the assay.

constraint	value
required	`True`

`operator_email`

Email address for the operator.

constraint	value
format	`email`
required	`True`

`pi`

Name of the principal investigator responsible for the data.

constraint	value
required	`True`

`pi_email`

Email address for the principal investigator.

constraint	value
format	`email`
required	`True`

`assay_category`

Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence.

constraint	value
enum	`mass_spectrometry_imaging`
required	`True`

`assay_type`

The specific type of assay being executed.

constraint	value
enum	`MIBI`
required	`True`

`analyte_class`

Analytes are the target molecules being measured with the assay.

constraint	value
enum	`protein`
required	`True`

`is_targeted`

Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay.

constraint	value
type	`boolean`
required	`True`

`acquisition_instrument_vendor`

An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.

constraint	value
required	`True`

`acquisition_instrument_model`

Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data.

constraint	value
required	`True`

Unique to this type

`number_of_antibodies`

Number of antibodies.

constraint	value
type	`integer`
required	`True`

`number_of_channels`

Number of fluorescent channels imaged during each cycle.

constraint	value
type	`integer`
required	`True`

`resolution_x_value`

The width of a pixel. (Akoya pixel is 377nm square)

constraint	value
type	`number`
required	`True`

`resolution_x_unit`

The unit of measurement of width of a pixel.(nm) Leave blank if not applicable.

constraint	value
enum	`mm`, `um`, or `nm`
required	`False`
required if	`resolution_x_value` present

`resolution_y_value`

The height of a pixel. (Akoya pixel is 377nm square)

constraint	value
type	`number`
required	`True`

`resolution_y_unit`

The unit of measurement of height of a pixel. (nm) Leave blank if not applicable.

constraint	value
enum	`mm`, `um`, or `nm`
required	`False`
required if	`resolution_y_value` present

`max_x_width_value`

Image width value of the ROI acquisition.

constraint	value
type	`number`
required	`True`

`max_x_width_unit`

Units of image width of the ROI acquisition. Leave blank if not applicable.

constraint	value
enum	`um`
required	`False`
required if	`max_x_width_value` present

`max_y_height_value`

Image height value of the ROI acquisition.

constraint	value
type	`number`
required	`True`

`max_y_height_unit`

Units of image height of the ROI acquisition. Leave blank if not applicable.

constraint	value
enum	`um`
required	`False`
required if	`max_y_height_value` present

`roi_description`

A description of the region of interest (ROI) captured in the image.

constraint	value
required	`True`

`roi_id`

Multiple images (1-n) are acquired from regions of interest (ROI1, ROI2, ROI3, etc) on a slide. The roi_id is a number from 1-n representing the ROI captured on a slide.

constraint	value
type	`integer`
required	`True`

`acquisition_id`

The acquisition_id refers to the directory containing the ROI images for a slide. Together, the acquisition_id and the roi_id indicate the slide-ROI represented in the image.

constraint	value
required	`True`

`area_normalized_ion_dose_unit`

Area normalized ion dose unit. Leave blank if not applicable.

constraint	value
enum	`nA*hr/mm2`
required	`False`
required if	`area_normalized_ion_dose_value` present

`area_normalized_ion_dose_value`

Number of primary ions delivered to the sample per unit area.

constraint	value
type	`number`
required	`True`

`data_precision_bytes`

Numerical data precision in bytes.

constraint	value
type	`number`
required	`True`

`dual_count_start`

Threshold for dual counting.

constraint	value
type	`number`
required	`True`

`end_datetime`

Time stamp indicating end of ablation for ROI.

constraint	value
type	`datetime`
format	`%Y-%m-%d %H:%M`
required	`True`

`pixel_dwell_time_value`

Resident time of primary ion beam on each pixel.

constraint	value
type	`number`
required	`True`

`pixel_dwell_time_unit`

Pixel dwell time unit. Leave blank if not applicable.

constraint	value
enum	`ms`
required	`False`
required if	`pixel_dwell_time_value` present

`pixel_size_x_value`

Width value of the pixel or voxel measurement (distinct from the image resolution_x_value).

constraint	value
type	`number`
required	`True`

`pixel_size_x_unit`

Width unit of the pixel or voxel measurement. Leave blank if not applicable.

constraint	value
enum	`nm`
required	`False`
required if	`pixel_size_x_value` present

`pixel_size_y_value`

Length value of the pixel or voxel measurement (distinct from the image resolution_y_value).

constraint	value
type	`number`
required	`True`

`pixel_size_y_unit`

Length unit of the pixel or voxel measurement. Leave blank if not applicable.

constraint	value
enum	`nm`
required	`False`
required if	`pixel_size_y_value` present

`preparation_instrument_vendor`

The manufacturer of the instrument used to prepare the sample for the assay.

constraint	value
enum	`Custom` or `Ionpath`
required	`True`

`preparation_instrument_model`

The model number/name of the instrument used to prepare the sample for the assay.

constraint	value
enum	`Custom`, `MIBIscope 1`, or `MIBIscope 2`
required	`True`

`primary_ion`

Primary ion.

constraint	value
enum	`Xe`
required	`True`

`primary_ion_current_value`

Primary ion current value.

constraint	value
type	`number`
required	`True`

`primary_ion_current_unit`

Primary ion current unit, typically nA or pA. Leave blank if not applicable.

constraint	value
enum	`nA` or `pA`
required	`False`
required if	`primary_ion_current_value` present

`reagent_prep_protocols_io_doi`

DOI for protocols.io referring to the protocol for preparing reagents for the assay.

constraint	value
required	`True`
pattern (regular expression)	`10\.17504/.*`
url	prefix: `https://dx.doi.org/`

`section_prep_protocols_io_doi`

DOI for protocols.io referring to the protocol for preparing tissue sections for the assay.

constraint	value
required	`True`
pattern (regular expression)	`10\.17504/.*`
url	prefix: `https://dx.doi.org/`

`segment_data_format`

This refers to the data type, which is a “float” for the IMC counts.

constraint	value
enum	`float`, `integer`, or `string`
required	`True`

`signal_type`

Type of signal measured per channel (usually dual counts)

constraint	value
enum	`dual count`, `pulse count`, or `intensity value`
required	`True`

`start_datetime`

Time stamp indicating start of ablation for ROI.

constraint	value
type	`datetime`
format	`%Y-%m-%d %H:%M`
required	`True`

`antibodies_path`

Relative path to file with antibody information for this dataset.

constraint	value
required	`True`

`contributors_path`

Relative path to file with ORCID IDs for contributors for this dataset.

constraint	value
required	`True`

`data_path`

Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions.

constraint	value
required	`True`

Directory schemas

Version 0.0 (use this one)

pattern	required?	description
`mcd/[^/]+_HuBMAP_[^/]+_slide[^/]+\.zip`		Zipped CSV containing labels for sections as well as whether or not they were included in the 3D model.
`mcd/section_report\.csv`		Contains tissue id, acquisition id, 3D image ordering, MCD image ordering, and boolean if used for 3D model.
`mcd/channelnames_report\.csv`	✓	Contains antibodies names used and whether they were detected sufficiently or not.
`3D_image_stack\.ome\.tiff`	✓	OME.tiff file comprising all slices and channels.
`SingleCellData/cells\.csv`	✓	Contains one csv file per tissue with marker intensities (untransformed, range normalized to 99th percentile), phenograph cluster label and cell type label per single cell.
`SingleCellData/cellsinfo\.txt`		Text file containing formatting information about cellsorgan.csv.
`Mapping/cluster_labels_image\.tif`	✓	Cell image labeled by cell type.
`processed/umap_phenograph\.pdf`		tSNE phenograph. File is optional.
`processed/CellTypeComposition_perTissue\.pdf`		Cell type composition bar graph per tissue. File is optional.
`processed/Densityplots_perMarker\.pdf`		[QA/QC] Density plots of marker intensity, separated by marker. File is optional.
`processed/celltypes\.pdf`		Heatmap of marker expression per cluster, annotated by assigned cell type. File is optional.
`extras\/.*`		Folder for general lab-specific files related to the dataset. [Exists in all assays]