omero-screen
Run the OMERO-Screen analysis pipeline on one or more plates.
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-stitchto 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
--stitchand 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
cpuwhen 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
noneto 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.