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Importing Volumes

SABER uses Copick to manage tomographic data. Copick provides a unified interface for accessing volumes whether they're stored locally, on an HPC cluster, or on the CryoET Data Portal.

Setting Up a Copick Project

Create a config pointing to a local directory where results will be written:

copick config filesystem \
    --overlay-root /path/to/overlay

To define biological objects at creation time (useful for particle picking workflows):

copick config filesystem \
    --overlay-root /path/to/overlay \
    --objects ribosome,True,130,6QZP \
    --objects apoferritin,True,65 \
    --objects membrane,False
What the generated config.json looks like 
{
    "name": "my_project",
    "description": "A test project.",
    "version": "1.0.0",

    "pickable_objects": [
        { "name": "ribosome",   "is_particle": true,  "label": 1, "radius": 130, "pdb_id": "6QZP" },
        { "name": "apoferritin","is_particle": true,  "label": 2, "radius": 65 },
        { "name": "membrane",   "is_particle": false, "label": 3 }
    ],

    "overlay_root": "local:///path/to/overlay",
    "overlay_fs_args": { "auto_mkdir": true },

    "static_root": "local:///path/to/static",
    "static_fs_args": { "auto_mkdir": true }
}

Overlay vs. Static root

The overlay root is writable — SABER writes segmentations, coordinates, and metadata here. The static root is read-only, intended for the original tomogram files that you never want to accidentally overwrite.

Link a project to a public dataset from the CryoET Data Portal:

copick config dataportal \
    --dataset-id DATASET_ID \
    --overlay-root /path/to/local/overlay

Pickable objects are automatically populated from the portal dataset. You only need to provide the dataset ID and a local path for writing results.

Finding your dataset ID

Browse datasets at cryoetdataportal.czscience.com and copy the numeric ID from the dataset URL.

Importing Local MRC Files

If you have tomograms processed with Warp, IMOD, AreTomo, or any other reconstruction pipeline, import them into Copick with:

copick add tomogram \
    --config config.json \
    --tomo-type denoised \
    --voxel-size 10 \
    --no-create-pyramid \
    'path/to/volumes/*.mrc'
Parameter Description
--tomo-type Tag for this reconstruction (denoised, wbp, filtered)
--voxel-size Voxel size in Å — SABER uses this for downsampling
--no-create-pyramid Skip multi-resolution pyramid (faster import)

Flat directory required

This command expects all .mrc files in a single flat directory. If your files are in nested subdirectories, see the Advanced Import guide.

Verifying Your Project

After import, confirm that Copick can see your tomograms:

import copick

root = copick.from_file("config.json")
print(f"Found {len(root.runs)} runs")

# Inspect the first run
run = root.runs[0]
print(run.name)
print([t.voxel_size for t in run.tomograms])

Next Steps