Imaging Channel
An Imaging Channel entry describes the channel-level metadata for a single detection channel within a multiplexed or multi-channel imaging experiment, such as a cycle in CODEX/CyCIF, a fluorescence channel in MxIF, or a metal-tagged channel in Imaging Mass Cytometry (IMC). Rather than describing an image file itself, this module captures the reagents, targets, and physical detection parameters (fluorophore, metal isotope, oligo barcode, excitation/emission wavelengths) associated with one channel, along with the antibody or probe used to generate signal in that channel.
Because a single imaging experiment can involve dozens of channels across multiple staining cycles, Imaging Channel entries are typically submitted as a table with one row per channel per assay, and are then linked from the imaging file-level modules (Imaging Level 1 and Imaging Level 2) via the ImagingChannel Key. This separation keeps channel/antibody metadata reusable and consistent across the many image files that share the same channel configuration.
Why You Should Contribute Imaging Channel Entries¶
Contributing Imaging Channel entries ensures that the antibodies, probes, and detection parameters behind each signal in a multiplexed image are fully traceable — which is essential for reproducing staining panels, troubleshooting failed channels, and enabling downstream re-analysis of multiplexed imaging data by other groups.
Who Should Be Contributing Imaging Channel Entries?¶
- Imaging Scientists – Document the antibody panel, fluorophore, or isotope assignments used to generate each channel of a multiplexed imaging experiment.
- Core Facility Staff – Record the reagent lot numbers, vendors, and detection settings applied during acquisition on shared imaging instrumentation.
- Computational Imaging Analysts – Ensure channel metadata is complete and consistent so that channel-to-marker mappings can be programmatically resolved during analysis.
- Lab Managers – Maintain a durable record of antibody clones, dilutions, and QC outcomes across staining cycles and experiments.
Download Template¶
You can download the ImagingChannel CSV template to streamline data entry.
Full Field Reference¶
Below is the full field reference table with attributes and their descriptions.
| Attribute | Description | Required | Column Type | Format | Regex Pattern | Standard Terms | Examples |
|---|---|---|---|---|---|---|---|
| ImagingChannel_id | Unique row identifier, used as a primary key for record updates. | True | string | None | None | None | |
| Study Key | The unique Study_id foreign keys associated with the resource, found in the grant Study information. Used to group the resource with other components. Please provide multiple values as a comma-separated list. | False | string | None | None | None | |
| Channel Identifier | This must match the corresponding field in the OME-XML / TIFF header. (eg 'Channel:0:1') | True | string | None | None | None | |
| Channel Name | This must match the corresponding field in the OME-XML / TIFF header. (eg 'Blue' or 'CD45' or 'E-cadherin') | True | string | None | None | None | |
| Channel Passed QC | Identify stains that did not pass QC but are included in the dataset. | False | string | None | None | View | |
| Channel Cycle Number | The cycle # in which the co-listed reagent(s) was(were) used. Integer >= 1 (up to number of cycles) | False | number | None | None | None | |
| Channel Sub-cycle Number | Sub cycle number | False | number | None | None | None | |
| Channel Antibody Role | Is this antibody acting as a primary or secondary antibody? | False | string | None | None | View | |
| Channel Target Name | Short descriptive name (abbreviation) for this target (antigen) | True | string | None | None | None | |
| Channel Antibody Name | Antibody Name (free text (eg “Keratin”, “CD163”, “DNA”)) | False | string | None | None | None | |
| Channel Resource ID | Research Resource Identifier (eg “RRID: AB_394606”) | False | string | None | None | None | |
| Channel Fluorophore | Fluorescent dye label (eg Alexa Fluor 488) | False | string | None | None | None | |
| Channel Antibody Clone | Clone | False | string | None | None | None | |
| Channel Antibody Lot | Lot number from vendor | False | string | None | None | None | |
| Channel Antibody Vendor | Vendor | False | string | None | None | None | |
| Channel Antibody Catalog Number | Catalog Number | False | string | None | None | None | |
| Channel Excitation Wavelength | Center/peak of the excitation spectrum (nm) | False | number | None | None | None | |
| Channel Emission Wavelength | Center/peak of the emission spectrum (nm) | False | number | None | None | None | |
| Channel Excitation Bandwidth | Nominal width of excitation spectrum (nm) | False | number | None | None | None | |
| Channel Emission Bandwidth | Nominal width of emission spectrum (nm) | False | number | None | None | None | |
| Channel Metal Symbol | Element abbreviation. eg “La” or “Nd” | False | string | None | None | View | |
| Channel Metal Isotope | Element mass number | False | number | None | None | None | |
| Channel Oligo Barcode Upper Strand | Oligo Barcode - Upper Strand | False | string | None | None | None | |
| Channel Oligo Barcode Lower Strand | Oligo Barcode - Lower Strand | False | string | None | None | None | |
| Channel Probe Dilution Ratio | Dilution (eg 1:1000) | False | string | None | None | None | |
| Channel Probe Concentration | Concentration (eg 10ug/mL) | False | string | None | None | None |