# omero-screen Run the OMERO-Screen analysis pipeline on one or more plates. ``` bash omero-screen [OPTIONS] ID...... ``` ID… are OMERO plate IDs. Each plate is segmented, measured and, where an EdU channel is present, assigned cell-cycle phases; results are attached back to the plate in OMERO. Setting up and checking an install: omero-screen setup configure the server, user and password omero-screen doctor check the installation omero-screen config show show the settings in effect omero-screen models pull SET / models publish MODEL.pt Full --help output Usage: omero-screen [OPTIONS] ID... Run the OMERO-Screen analysis pipeline on one or more plates. ID... are OMERO plate IDs. Each plate is segmented, measured and, where an EdU channel is present, assigned cell-cycle phases; results are attached back to the plate in OMERO. Setting up and checking an install: omero-screen setup configure the server, user and password omero-screen doctor check the installation omero-screen config show show the settings in effect omero-screen models pull SET / models publish MODEL.pt Options: --version Show the version and exit. --env TEXT Environment name (requires configuration file .env.{name}). --config PATH Path to an OMERO_SCREEN_CONFIG JSON (MODEL_DICT / FEATURELIST / CHANNEL_SEG_PROFILES). Overrides the OMERO_SCREEN_CONFIG env var. Errors if the path does not exist (no silent fallback to defaults). --inference MODEL Inference model filename(s). Accepts one or more values. --gallery INTEGER Width N for the inference NxN example gallery. [default: 10] --batch INTEGER Classification batch size. [default: 16] --segmentation / --no-segmentation Only perform image segmentation. [default: no-segmentation] --delete Delete the plate's existing segmentation masks and segment from scratch. Without this, a re-run reuses the stored masks (both stitched and per-field) and only recomputes the measurements. Use it after changing segmentation settings, or to repair a plate whose stored masks are wrong or empty. --cp4 Use Cellpose 4 (cpsam) for segmentation instead of the default Cellpose 3 models. --model MODEL Override all segmentation models with a single model name (e.g. 'cp4:cpsam', 'cp3:cyto3'). Overrides --cp4. --benchmark / --no-benchmark Record per-image timing data and write a JSON benchmark report. [default: no- benchmark] --stitch / --no-stitch Run stitched-well segmentation: assemble all fields per well into one canvas, segment that canvas, and exclude border objects only at the outer edge. [default: no-stitch] --stream-stitch / --no-stream-stitch Stitch one timepoint at a time to bound host RAM on long multi-channel timelapses (peak ~= canvas + one frame, not all fields + canvas; costs n_fields x T OMERO reads). Default: auto-enable when the estimated peak exceeds the host-RAM budget. Use --stream- stitch / --no-stream-stitch to force. Requires --stitch. --stitch-config PATH Path to an OMERO_SCREEN_STITCH_CONFIG JSON configuration. Overrides the OMERO_SCREEN_STITCH_CONFIG env var. Errors if the path does not exist (no silent fallback to defaults). --track MODEL Track nuclei across time with Trackastra. Optional MODEL is a pretrained name or checkpoint path (default when flag given: general_2d). Requires --stitch and a timelapse (T>1); a no-op on single-timepoint plates. --track-mode [greedy|greedy_nodiv|ilp] Trackastra linking mode. [default: greedy] --track-batch-size INTEGER Attention windows Trackastra scores per forward pass. Caps GPU memory during tracking; lower this if tracking hits CUDA OOM, raise it for faster scoring when VRAM allows (Trackastra's own GPU default is 16). [default: 4] --track-device [cpu|cuda] Force the tracking device (default: auto- detect). Use 'cpu' when a dense well exceeds GPU VRAM -- runs the identical computation in host RAM (slower, but no 44 GiB ceiling and no loss of accuracy). --track-window INTEGER Override Trackastra's temporal window (frames per attention window). Smaller cuts GPU memory ~quadratically at the cost of temporal context; default keeps the model's trained window. --log-level TEXT Log level (DEBUG/INFO/WARNING/ERROR). Overrides $OMERO_SCREEN_LOG_LEVEL; default INFO. --log-file TEXT Log file path, or 'none' to disable file logging. Overrides $OMERO_SCREEN_LOG_FILE; default logs/app.log. -v, --verbose Verbose debugging: DEBUG level, console logging on, and rich tracebacks. Console is off by default so logs don't clutter the progress display. --help Show this message and exit. # Arguments `ID…: INTEGER` Required. # Options `--version` Show the version and exit. `--env: TEXT` Environment name (requires configuration file .env.{name}). `--config: FILE` Path to an OMERO_SCREEN_CONFIG JSON (MODEL_DICT / FEATURELIST / CHANNEL_SEG_PROFILES). Overrides the OMERO_SCREEN_CONFIG env var. Errors if the path does not exist (no silent fallback to defaults). `--inference: TEXT` Inference model filename(s). Accepts one or more values. `--gallery: INTEGER = 10` Width N for the inference NxN example gallery. `--batch: INTEGER = 16` Classification batch size. `--segmentation, --no-segmentation` Only perform image segmentation. `--delete` Delete the plate's existing segmentation masks and segment from scratch. Without this, a re-run reuses the stored masks (both stitched and per-field) and only recomputes the measurements. Use it after changing segmentation settings, or to repair a plate whose stored masks are wrong or empty. `--cp4` Use Cellpose 4 (cpsam) for segmentation instead of the default Cellpose 3 models. `--model: TEXT` Override all segmentation models with a single model name (e.g. `cp4:cpsam`, `cp3:cyto3`). Overrides `--cp4`. `--benchmark, --no-benchmark` Record per-image timing data and write a JSON benchmark report. `--stitch, --no-stitch` Run stitched-well segmentation: assemble all fields per well into one canvas, segment that canvas, and exclude border objects only at the outer edge. `--stream-stitch, --no-stream-stitch` Stitch one timepoint at a time to bound host RAM on long multi-channel timelapses (peak ~= canvas + one frame, not all fields + canvas; costs n_fields x T OMERO reads). Default: auto-enable when the estimated peak exceeds the host-RAM budget. Use `--stream-stitch` / `--no-stream-stitch` to force. Requires `--stitch`. `--stitch-config: FILE` Path to an OMERO_SCREEN_STITCH_CONFIG JSON configuration. Overrides the OMERO_SCREEN_STITCH_CONFIG env var. Errors if the path does not exist (no silent fallback to defaults). `--track: TEXT` Track nuclei across time with Trackastra. Optional MODEL is a pretrained name or checkpoint path (default when flag given: general_2d). Requires `--stitch` and a timelapse (T\>1); a no-op on single-timepoint plates. `--track-mode: CHOICE = greedy` Trackastra linking mode. `--track-batch-size: INTEGER = 4` Attention windows Trackastra scores per forward pass. Caps GPU memory during tracking; lower this if tracking hits CUDA OOM, raise it for faster scoring when VRAM allows (Trackastra's own GPU default is 16). `--track-device: CHOICE` Force the tracking device (default: auto-detect). Use `cpu` when a dense well exceeds GPU VRAM -- runs the identical computation in host RAM (slower, but no 44 GiB ceiling and no loss of accuracy). `--track-window: INTEGER` Override Trackastra's temporal window (frames per attention window). Smaller cuts GPU memory ~quadratically at the cost of temporal context; default keeps the model's trained window. `--log-level: TEXT` Log level (DEBUG/INFO/WARNING/ERROR). Overrides \$OMERO_SCREEN_LOG_LEVEL; default INFO. `--log-file: TEXT` Log file path, or `none` to disable file logging. Overrides \$OMERO_SCREEN_LOG_FILE; default logs/app.log. `-v, --verbose` Verbose debugging: DEBUG level, console logging on, and rich tracebacks. Console is off by default so logs don't clutter the progress display.