Imaging Level 3 (Image)
An Imaging Level 3 (Image) entry describes quality-controlled or co-registered image data — imagery that has been processed beyond the raw and pre-processed stages to correct artifacts, align channels or cycles, and confirm suitability for downstream analysis. It carries the same detailed image-format metadata as Imaging Level 2 (optical parameters, pixel dimensions, pyramid/Z-stack/timeseries flags, and pixel encoding), reflecting the state of the image after QC and/or co-registration have been applied.
Imaging Level 3 (Image) entries link back to the pre-processed image via ImagingLevel2 Key and to the relevant channel via ImagingChannel Key, preserving a clear processing lineage from raw acquisition through to analysis-ready imagery. This level typically serves as the direct input to segmentation (Imaging Level 3 Segments) and downstream feature extraction (Imaging Level 4).
Why You Should Contribute Imaging Level 3 (Image) Entries¶
Contributing Imaging Level 3 (Image) entries ensures that quality-controlled and co-registered imagery is clearly distinguished from raw data, with full traceability back to its source image — supporting confident reuse of processed images in downstream segmentation and analysis.
Who Should Be Contributing Imaging Level 3 (Image) Entries?¶
- Computational Imaging Analysts – Document QC and co-registration outcomes and the resulting processed image files.
- Imaging Scientists – Verify that processing steps applied to raw images are accurately reflected in the metadata.
- Core Facility Staff – Confirm image quality metrics and processing parameters used prior to downstream analysis.
- Data Managers – Track processed image files to maintain a complete and auditable imaging data lineage.
Download Template¶
You can download the ImagingLevel3Image 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 |
|---|---|---|---|---|---|---|---|
| ImagingLevel3Image_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 | |
| 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 | |
| ImagingLevel2 Key | Unique ImagingLevel2_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 | |
| 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 | |
| Image Objective | Objective lens identifier | False | string | None | None | None | |
| Image Nominal Magnification | The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units) | False | number | None | None | None | |
| Image Lense Aperture | The numerical aperture of the lens. Floating point value > 0. | False | number | None | None | None | |
| Image Working Distance | The working distance of the lens, expressed as a floating point number. Floating point > 0. | False | number | None | None | None | |
| Image Working Distance Unit | The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um) | False | string | None | None | View | |
| Image Immersion Type | Immersion medium | False | string | None | None | View | |
| Image Pyramidal | Does data file contain pyramid of images | False | boolean | None | None | View | |
| Image Z stack | Does data file contain a Z-stack of images | False | boolean | None | None | None | |
| Image Timeseries | Does data file contain a time-series of images | False | boolean | None | None | None | |
| Image FOV Index | Index of FOV (as it pertains to its sequence order). Integer >= 1 | False | number | None | None | None | |
| Image FOV Size X | Field of view X dimension. Floating point | False | number | None | None | None | |
| Image FOV Size X Unit | Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um) | False | string | None | None | None | |
| Image FOV Size Y | Field of view Y dimension. Floating point value | False | number | None | None | None | |
| Image FOV Size Y Unit | Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um) | False | string | None | None | None | |
| Image Frame Averaging | Number of frames averaged together (if no averaging, set to 1). Integer >= 1 | False | number | None | None | None | |
| Image Identifier | Unique internal image identifier. eg "Image:0". (To be extracted from OME-XML) | False | string | None | None | None | |
| Image Dimension Order | The order in which the individual planes of data are interleaved. | False | string | None | None | None | |
| Image Physical Size X | Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0. | False | number | None | None | None | |
| Image Physical Size X Unit | The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um) | False | string | None | None | None | |
| Image Physical Size Y | Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0. | False | number | None | None | None | |
| Image Physical Size Y Unit | The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um) | False | string | None | None | None | |
| Image Physical Size Z | Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0. | False | number | None | None | None | |
| Image Physical Size Z Unit | The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um) | False | string | None | None | None | |
| Image Pixels BigEndian | Boolean (True/False) | False | boolean | None | None | View | |
| Image Plane Count | Number of Z-planes (not to be confused with downsampled "pyramid"). Integer >=1 | False | number | None | None | None | |
| Image Channel Size | Number of channels. Integer >= 1 | False | number | None | None | None | |
| Image Number of Timepoints | Number of time points. Integer >= 1 | False | number | None | None | None | |
| Image X Pixels | Size of image: X dimension (in pixels). Integer >= 1 | False | number | None | None | None | |
| Image Y Pixels | Size of image: Y dimension (in pixels). Integer >= 1 | False | number | None | None | None | |
| Image Z Pixels | Size of image: Z dimension (in pixels). Integer >= 1 | False | number | None | None | None | |
| Image Pixel Type | Data type for each pixel value. E.g. "uint16" | False | string | None | None | None |