Extractors – Metadata overview¶
OpenEM extractors read metadata from microscope files and sidecar files, convert it to structured JSON, and validate it against an OSC-EM schema. The Ingestor combines the result with your entries before registering the dataset in SciCat.
How extraction works¶
In step 1 of the Ingestor workflow, select the dataset directory and the matching extraction method. The extractor then:
- searches the directory for supported files;
- extracts and converts the available metadata; and
- displays the validated result for you to review and complete.
An empty field does not necessarily mean that the information does not apply. It may be absent from the source files or require facility configuration or manual input.
Choose an extraction method¶
The methods available in the Ingestor depend on your facility's configuration.
| Method | Use for | Supported input |
|---|---|---|
| Life Science | Single-particle and cryo-electron tomography data | SerialEM, EPU and TOMO5 metadata |
| Materials Science | Materials-science EM data | One .emd or .prz file per dataset directory |
For supported versions, setup requirements and limitations, see the Life Science extractor or the Materials Science extractor. If the suitable method is unavailable, contact local support.
OSC-EM schema profiles¶
Choose the profile that describes the experiment. The linked OSC-EM pages are the authoritative reference for fields, required values, units and allowed values.
| Profile | Scope | OSC-EM reference |
|---|---|---|
| General | TEM, STEM, EELS, EDX and general materials science | General schema |
| SPA | Single-particle cryo-EM acquisition and processing | SPA schema |
| Subtomogram Averaging | Molecular cryo-electron tomography | Subtomogram schema |
| Environmental Tomography | Tomography of environmental samples | Environmental tomography schema |
| Cellular Tomography | Tomography of cultured cells or tissue | Cellular tomography schema |
Useful definitions:
- Acquisition and instrument
- Sample and specimen
- People and funding
- SPA processing
- Tomography acquisition
- Environmental samples and cellular samples
- Values and SI units
- Downloadable schema artifacts and versions
Before continuing¶
Check that the extraction method and schema profile match the experiment, then review the extracted microscope, acquisition and unit values. Complete the scientific context, sample and ownership information that cannot be read from the files. The final JSON is shown again in the confirmation step.
If metadata is missing or validation fails, verify that you selected the correct directory and method, then follow the displayed validation message. Contact support with the extraction method, source format, affected field and exact error message if the problem remains.