omero-train CLI

Note

The full option detail for every omero-train command — flags, defaults, arguments and types — is generated directly from the code in the CLI reference. This page covers what the tool is for and how it is used in practice; go to the generated pages for the exact switches.

What this tool does

omero-train is a command-line tool that lets you manage your training database, inspect annotation statistics, and export data — without opening Napari. It is useful for:

Quickly checking how many cells have been labelled for a classifier.
Exporting annotation data to CSV for downstream analysis or sharing with collaborators.
Cleaning up classifiers or sessions that are no longer needed.
Migrating training data created before the database was introduced.

Installation

omero-train is installed automatically as part of omero-screen-napari. After installation, it is available in your terminal:

omero-train --help

Commands overview

Command	What it does
`list`	Show all classifiers with summary statistics
`stats`	Show detailed statistics for one classifier
`export`	Export annotations to CSV, JSON, or Parquet
`delete`	Remove a classifier and its sessions
`migrate`	Import existing NPY files into the database (for legacy data)

`omero-train list`

Lists all classifiers in the training database with a summary table.

omero-train list

Output columns:

Column	Description
ID	Internal database ID
Name	Classifier name
Sessions	Number of annotation sessions
Annotations	Total crops labelled
Classes	Class names defined for this classifier
Created	Date the classifier was first created

Example output:

┌────┬─────────────┬──────────┬─────────────┬──────────────────────────────────┐
│ ID │ Name        │ Sessions │ Annotations │ Classes                          │
├────┼─────────────┼──────────┼─────────────┼──────────────────────────────────┤
│  1 │ mitosis-rpe │        4 │         320 │ interphase, mitosis, apoptosis   │
│  2 │ drug-u2os   │        2 │         150 │ normal, stressed                 │
└────┴─────────────┴──────────┴─────────────┴──────────────────────────────────┘

`omero-train stats`

Shows detailed statistics for a single classifier, identified by name or database ID.

omero-train stats <name-or-id>

Examples:

omero-train stats mitosis-rpe
omero-train stats 1

Output includes: - General info (ID, total sessions, total annotations, classes) - Class distribution table with counts and percentages - Per-session breakdown (plate, well, images, timepoint, cell cycle filter, cell count, class distribution)

Example output:

Classifier: mitosis-rpe
Sessions: 4  |  Total cells: 320  |  Classes: interphase, mitosis, apoptosis

Class Distribution
┌─────────────┬───────┬────────────┐
│ Class       │ Count │ Percentage │
├─────────────┼───────┼────────────┤
│ interphase  │   224 │      70.0% │
│ mitosis     │    80 │      25.0% │
│ apoptosis   │    16 │       5.0% │
│ unassigned  │     0 │       0.0% │
└─────────────┴───────┴────────────┘

Sessions
┌────┬──────────┬──────┬────────┬──────────────┬────────┬───────────────┐
│ ID │ Plate ID │ Well │ Images │ Cell Cycle   │ Cells  │ Distribution  │
├────┼──────────┼──────┼────────┼──────────────┼────────┼───────────────┤
│  1 │     3869 │ E2   │ All    │ All          │     80 │ interph.: 60  │
│  2 │     3869 │ F3   │ 0, 1   │ All          │     80 │ mitosis: 20   │
└────┴──────────┴──────┴────────┴──────────────┴────────┴───────────────┘

`omero-train export`

Exports all annotations for a classifier to a file. Useful for sharing data, computing statistics in R or Python, or backing up before deletion.

omero-train export <name-or-id> [options]

You can choose the output format, set the output path, and restrict the export to a single plate or well — see omero-train export for the option list and defaults.

Examples:

# Export everything to CSV
omero-train export mitosis-rpe

# Export to JSON with a custom filename
omero-train export mitosis-rpe --format json --output ~/Desktop/mitosis_data.json

# Export only data from plate 3869
omero-train export mitosis-rpe --plate 3869

# Export only well A1 from plate 3869
omero-train export mitosis-rpe --plate 3869 --well A1

Output columns (CSV):

Column	Description
session_id	Database ID of the session
plate_id	OMERO plate ID
well	Well position
image_id	OMERO image ID
timepoint	Timepoint index
cell_index	Index of the crop within the session
class_label	Assigned class name
centroid_row	Row coordinate of the cell centroid in the full image
centroid_col	Column coordinate of the cell centroid

`omero-train delete`

Removes one or more classifiers and all their associated sessions and annotation records. This also deletes the NPY data files from disk.

omero-train delete <name-or-id> [<name-or-id> ...] [options]

You can skip the confirmation prompt, or delete only the sessions belonging to one plate — see omero-train delete for the option list.

Examples:

# Delete a single classifier (will ask for confirmation)
omero-train delete mitosis-rpe

# Delete without confirmation prompt
omero-train delete mitosis-rpe --yes

# Delete only the sessions from plate 3869, keep the classifier and other sessions
omero-train delete mitosis-rpe --plate 3869

# Delete multiple classifiers at once
omero-train delete mitosis-rpe drug-u2os --yes

Warning

Deletion is permanent. Export your data first with omero-train export if you may need it later.

`omero-train migrate`

Imports existing NPY training data files (created before the database was introduced) into the training database. This is a one-time operation for legacy data.

omero-train migrate [options]

You can point the scan at a different root directory, or preview the import without writing anything — see omero-train migrate for the option list and defaults.

Examples:

# Preview what would be migrated without making any changes
omero-train migrate --dry-run

# Run the migration from the default location
omero-train migrate

# Run from a custom directory
omero-train migrate --path /data/training_backup

The command scans the directory tree for .npy files and metadata.json files, infers the classifier structure from the folder layout, and creates the corresponding database records.

Where is the database?

The training database is an SQLite file stored at:

~/omeroscreen_trainingdata/training_data.db

You can open this file with any SQLite browser (e.g. DB Browser for SQLite) if you want to query the data directly.

Tips

Run omero-train list regularly to get a quick health check on your training data.
Before deleting anything, always run omero-train export first.
Use omero-train stats to check class balance before starting a training run — heavily imbalanced classes (e.g. 95% interphase, 5% mitosis) may need more data for the rare class.
The --plate filter on both export and delete is useful when one plate’s data turned out to be low quality and you want to remove it without losing everything else.