Imaging Level 3 (Segments)
An Imaging Level 3 (Segments) entry describes image segmentation mask information — the output of algorithms that delineate objects of interest (such as nuclei, cytoplasm, plasma membrane, or whole cells) within a processed image. Rather than pixel intensity data, this module captures how segmentation results are stored (mask, outline, polygon, probability map, or point representation), the object class being segmented, the number of objects identified, and a pointer to the parameter file needed to reproduce the segmentation.
Imaging Level 3 (Segments) entries link to both the pre-processed image (ImagingLevel2 Key) and the QC'd/co-registered image (ImagingLevel3Image Key) that the segmentation was derived from. Segmentation results documented here are typically the direct input to object-level feature extraction and summary statistics captured in Imaging Level 4.
Why You Should Contribute Imaging Level 3 (Segments) Entries¶
Contributing Imaging Level 3 (Segments) entries ensures that segmentation outputs — and the parameters used to generate them — are documented clearly enough for others to reproduce, validate, or build on object-level analyses without re-running segmentation from scratch.
Who Should Be Contributing Imaging Level 3 (Segments) Entries?¶
- Computational Imaging Analysts – Document segmentation algorithms, parameters, and resulting object classes and counts.
- Imaging Scientists – Confirm that the object classes and segmentation representations accurately reflect the underlying biology.
- Core Facility Staff – Provide context on the imaging assay driving segmentation choices (e.g. nuclear vs. whole-cell masks).
- Data Managers – Track segmentation output files and their associated parameter files for reproducibility.
Download Template¶
You can download the ImagingLevel3Segments 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 |
|---|---|---|---|---|---|---|---|
| ImagingLevel3Segments_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 | |
| 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 | |
| ImagingLevel3Image Key | Unique ImagingLevel3Image_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 Segmentation Data Type | Specifies how the segmentation is stored | True | string | None | None | View | |
| Image Parameter file | Path in Synapse to a text file listing algorithm version numbers and relevant parameters needed to reproduce the analysis | False | string | None | None | None | |
| Software and Version | Name of software used to generate the information contained in the file. String | False | string | None | None | None | |
| Image Object Class | Defines the structure that the mask delineates | False | string | None | None | View | |
| Image Object Class Description | If Imaging Object Class is "Other", please use this field to provide a text description of the imaging object class associated with the segmentation data | False | string | None | None | None | |
| Image Number of Objects | The number of objects (eg cells) described | False | number | None | None | None |