Imaging Level 1
An Imaging Level 1 entry describes a raw imaging data file — the unprocessed output of a microscope, scanner, or other imaging platform, prior to any quality control, co-registration, or downstream processing. This is the earliest and most complete record of what was captured during an imaging experiment, and includes the acquisition context (assay type, platform model and manufacturer, acquisition software, protocol link) along with standard file-level descriptors such as file format, species, and design.
Because raw images are typically generated per-channel or per-acquisition, Imaging Level 1 entries link back to the corresponding channel metadata via the ImagingChannel Key, and forward to the biospecimen that was imaged via Biospecimen Key. This level anchors the full imaging data provenance chain: every downstream processed image, segmentation, or feature array (Imaging Levels 2–4) traces back to the raw file(s) documented here.
Why You Should Contribute Imaging Level 1 Entries¶
Contributing Imaging Level 1 entries ensures that raw imaging outputs are properly cataloged, discoverable, and traceable back to the specimen and acquisition settings that produced them — the foundation that all subsequent image processing and analysis depends on.
Who Should Be Contributing Imaging Level 1 Entries?¶
- Imaging Scientists – Document raw image files and the acquisition settings used to generate them.
- Core Facility Staff – Record platform, instrument, and software details at the point of image acquisition.
- Computational Imaging Analysts – Ensure raw file metadata is complete so it can be correctly linked to downstream processed and derived imaging products.
- Data Managers – Track raw imaging files as they are deposited to ensure completeness of the imaging data provenance chain.
Download Template¶
You can download the ImagingLevel1 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 |
|---|---|---|---|---|---|---|---|
| ImagingLevel1_id | Unique row identifier, used as a primary key for record updates. This should be equivalent to the file Synapse Id unless otherwise indicated. | True | string | None | ^syn\d{7,8}$ | None | |
| Filename | The path of a file in Synapse, relative to the project. The file associated with the path will be annotated with attributes contained in this sheet. | False | string | None | None | None | |
| Biospecimen Key | Unique Biospecimen_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list. | False | string | None | -B\d{1,9} | 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 | |
| DatasetView Key | Unique DatasetView_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list. | False | string | None | None | None | |
| File Alias | A string identifier associated with the file. Must be unique. Can be the repository accesssion number (e.g., Synapse ID, GEO identifier such as GSE12345). No Greek Letters or DOIs. | True | string | None | None | None | |
| File Description | Description of the file. | False | string | None | None | None | |
| File Design | The overall design of the dataset or file, including a batch identifier, if applicable. | False | string | None | None | None | |
| File Level | The processing level the file can be mapped to. | True | string | None | None | View | |
| File Assay | The assay the file is representative of. | True | string | None | None | View | |
| File Species | The species the data was collected on. | True | string | None | None | View | |
| File Url | The url of where the file is stored. | True | string | uri | None | None | |
| File Format | The format of the file described by this entry. | True | string | None | None | View | |
| File Data Use Codes | DUO code - A data item that is used to indicate consent permissions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Available DUO code definitions can be found here: https://mc2-center.github.io/data-models/valid_values/study/#attribute-study-data-use-codes | False | string_list | None | None | None | |
| File Longitudinal Group | A label that can be used to identify groups of files from the same longitudinal/time-resolved experiment | False | string | None | None | None | |
| File Longitudinal Event Type | The type of event to which File Longitudinal Total Time Elapsed is related | False | string | None | None | View | |
| File Longitudinal Sequence Identifier | The order in which this file was collected with respect to the longitudinal experiment (e.g., 1, 2, etc.). Integer. | False | number | None | None | None | |
| File Longitudinal Time Elapsed Unit | The unit of time associated with Sequential and Total Time Elapsed attributes. | False | string | None | None | None | |
| File Longitudinal Total Time Elapsed | The total time elapsed between the first and current files contained this longitudinal group. | False | number | None | None | None | |
| Image Assay Type | Type of imaging assay | True | string | None | None | View | |
| Image Protocol Link | Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated. | False | string | uri | None | None | |
| Image Platform Model | The specific model of the instrument used to carry out an imaging experiment. | False | string | None | None | None | |
| Image Platform Manufacturer | Producer of the imaging equipment that was used to generate the digital image | False | string | None | None | None | |
| Image Software | The name of the software package that was used to capture, generate, and process the image. | False | string | None | None | None | |
| ImagingChannel Key | Unique ImagingChannel_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list. | False | string | None | None | None |