# omero-train CLI > **Note: 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](../reference/cli/index.md). 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: ``` bash omero-train --help ``` # Commands overview | Command | What it does | |----|----| | [`list`](../reference/cli/list.md) | Show all classifiers with summary statistics | | [`stats`](../reference/cli/stats.md) | Show detailed statistics for one classifier | | [`export`](../reference/cli/export.md) | Export annotations to CSV, JSON, or Parquet | | [`delete`](../reference/cli/delete.md) | Remove a classifier and its sessions | | [`migrate`](../reference/cli/migrate.md) | Import existing NPY files into the database (for legacy data) | ------------------------------------------------------------------------ # `omero-train list` Lists all classifiers in the training database with a summary table. ``` bash 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. ``` bash omero-train stats ``` **Examples:** ``` bash 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. ``` bash omero-train export [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`](../reference/cli/export.md) for the option list and defaults. **Examples:** ``` bash # 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. ``` bash omero-train delete [ ...] [options] ``` You can skip the confirmation prompt, or delete only the sessions belonging to one plate -- see [`omero-train delete`](../reference/cli/delete.md) for the option list. **Examples:** ``` bash # 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: 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. ``` bash 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`](../reference/cli/migrate.md) for the option list and defaults. **Examples:** ``` bash # 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](https://sqlitebrowser.org/)) 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.