Contribute Data to the Portal¶

The CryoET Data Portal supports a rapidly growing cryoET data corpus because of generous contributions from researchers like you!

Submission and Publication Process¶

1. Read our data submission policy (all data has a CC0 license) and data schema to learn how data is shared and organized on the Portal.

2. Review the metadata requirements to understand the requirements of data submission.

3. Contact us and we’ll reach out with next steps.

Metadata Requirements¶

Glossary¶

• Deposition: Depositions are collections of datasets, annotations, and/or (in the future) tomograms contributed by the same author(s). The website currently shows only depositions that include annotations. Click here for an example

• Dataset: Datasets are contributed sets of files associated with imaging one sample type with the same experimental conditions. Click here for an example

• Run: A tomography run is a collection of all data and annotations related to one physical location in a sample and is associated with a dataset that typically contains many other runs. Click here for an example

Contribution of Full Datasets¶

Deposition (Dataset Group)¶

Dataset group depositions contain 1 or more datasets.

Required Metadata

• Title

• Description (1-5 sentences)

• Authors (Name, ORCID, email, whether primary or corresponding)

• Cross-References (DOI, EMPIAR, EMDB, PDB)

Dataset¶

Required Metadata

• Title

• Description (1-5 sentences)

• Authors (Name, ORCID, email, whether primary or corresponding)

• Cross-References (DOI, EMPIAR, EMDB, PDB)

• Funding Information (Agency Name, Grant ID)

• Sample Type, one of:

  • cell

  • tissue

  • organism

  • organelle

  • virus

  • in_vitro

  • in_silico

  • other

• Description of sample preparation (steps separated by +)

• Description of grid preparation (steps separated by +)

• Description of other information not captured above

• Organism Name, ID (NCBI taxID)

• If cell:

  • Cell Type Name, ID (cell ontology)

  • Strain Name, ID

• If tissue:

  • Tissue Name, ID (UBERON identifier)

• If organelle:

  • Cell Component Name, ID (Gene Ontology)

Optional Metadata

• File/URL: Key photo for the website

Movie Stacks / Acquisition¶

Required Metadata per Run

• Files: Movie stacks in MRC, TIFF or EER format (or as listed, compressed)

  • Should be able to be associated to a Run by file name or location

• File: 1 MDOC file per run or similar (indicating mapping to tilt series and tilt order)

  • Should be able to be associated to a Run by file name or location

• Whether already gain corrected (True/False)

• Acceleration Voltage

• Spherical Abberation

• Tilt range (min, max)

• Tilt Step

• Tilt Scheme

• dose per movie stack (preferred) or Total Dose per Run

• Acquisition software

• Camera manufacturer and model

• Microscope manufacturer and model

• Microscope optical setup

  • Energy Filter Name

  • Image Corrector Type

  • Phase Plate Type

• Pixel Size (if not correct in file header)

Optional Metadata

• Files: Gain reference in MRC, DM4, GAIN format

  • Should be able to be associated with a Run (e.g. provide CSV-mapping of run name to gain name)

Tilt Series (Required per Run)¶

Required Metadata per Run

• File: 1 Assembled tilt series in MRC or OME-Zarr format

  • Should be able to be associated to a Run by file name or location

• File: Tilt angles in assembled tilt series in RAWTLT format (textfile, one angle per line)

  • Should be able to be associated to a Run by file name or location

• Authors (Name, ORCID, email, whether primary or corresponding)

• Binning from frames

• Pixel size (if not correct in header)

• Tilt axis rotation

• Whether is already transformed according to alignment in 2D

Optional Metadata

• Subjective quality rating according to this scale

Alignment (Required per Run)¶

Required Metadata per Run

• Files:

  • If aligned in IMOD (global alignments)

    • Required: XF file

    • Required: TLT file

    • Optional: XTILT file, tilt.com file, newst.com file

  • If aligned in AreTomo3:

    • Required: ALN-File

• Method type, one of:

  • fiducial based

  • patch tracking

  • projection matching

• Alignment type, one of:

  • Global (rigid transformations only)

  • Local (non-rigid transformations)

• Any alignment parameters not captured by the alignment file

  • Tilt offset

  • Volume origin offset

  • X-tilt offset

Tomograms (optional)¶

Required Metadata per Run

• File: at least one tomogram in MRC or OME-Zarr format

  • Should be able to be associated to a Run by file name or location

• Voxel size

• Ctf-corrected (True/False)

• Reconstruction method

• Reconstruction software

• Post-Processing (e.g. raw, denoised, filtered)

• Processing software

Annotations (optional)¶

Required Metadata per Annotated Object

• Object name

• Object ID (Gene Ontology or UniprotKB accession number)

Optional Metadata per Annotated Object

• Object state

• Object description

Required Metadata per Annotation File

• File: Annotation in MRC, OME-Zarr, STAR (RELION, STOPGAP), CSV, GLB, STL, OBJ, VTK format

  • At the same size, alignment, voxel spacing as one of the submitted tomograms.

• Authors (Name, ORCID, email, whether primary or corresponding)

• Cross-References (DOI, EMPIAR, EMDB, PDB)

• Can be considered ground truth (True/False)

• Annotation method

  • Description (steps separated by +)

  • Annotation software

  • Method links

  • Method type, one of:

    • Manual

    • Hybrid

    • Automated

    • Simulated

Contribution of Annotations for Existing Datasets¶

Deposition (Annotation Group)¶

Annotation group depositions contain annotations for one or more existing datasets

Required Metadata

• Title

• Description (1-5 sentences)

• Authors (Name, ORCID, email, whether primary or corresponding)

• Cross-References (DOI, EMPIAR, EMDB, PDB)

Annotations¶

Required Metadata per Annotated Object

• Object name

• Object ID (Gene Ontology or UniprotKB accession number)

• Object state

Optional Metadata per Annotated Object

• Object description

Required Metadata per Annotation File

• File: Annotation in MRC, OME-Zarr, STAR (RELION, STOPGAP), CSV, GLB, STL, OBJ, VTK format

  • At the same size, alignment, voxel spacing as one of the existing tomograms.

• Authors (Name, ORCID, email, whether primary or corresponding)

• Cross-References (DOI, EMPIAR, EMDB, PDB)

• Can be considered ground truth (True/False)

• Annotation method

  • Description (steps separated by +)

  • Annotation software

  • Method links

  • Method type, one of:

    • Manual

    • Hybrid

    • Automated

    • Simulated

Contribution of Tomograms for Existing Datasets¶

Deposition (Tomogram Group)¶

Tomogram group depositions contain 1 or more tomograms for an existing dataset.

Required Metadata

• Title

• Description (1-5 sentences)

• Authors (Name, ORCID, email, whether primary or corresponding)

• Cross-References (DOI, EMPIAR, EMDB, PDB)

Tomograms (Required per Run)¶

Required Metadata per Run

• File: at least one tomogram in MRC or OME-Zarr format

  • Should be able to be associated to a Run by file name or location

• Voxel size

• Ctf-corrected (True/False)

• Reconstruction method

• Reconstruction software

• Post-Processing (e.g. raw, denoised, filtered)

• Processing software

Alignment (Required if New)¶

If none of the existing alignments was used, it is required to submit the new alignment along with the tomograms.

Required Metadata per Run

• Files:

  • If aligned in IMOD (global alignments)

    • Required: XF file

    • Required: TLT file

    • Optional: XTILT file, tilt.com file, newst.com file

  • If aligned in AreTomo:

    • Required: ALN-File

• Method type, one of:

  • fiducial based

  • patch tracking

  • projection matching

• Alignment type, one of:

  • Global (rigid transformations only)

  • Local (non-rigid transformations)

• Any alignment parameters not captured by the alignment file, e.g.

  • Tilt offset

  • Volume origin offset

  • X-tilt offset