CLI

ultrack flow

Adds coordinates shift (vector field) to segmentation hypotheses.

ultrack flow [OPTIONS] [PATHS]...

Options

-r, --reader-plugin <reader_plugin>

Napari reader plugin.

Default:

napari

-cfg, --config <config>

Required Ultrack configuration file (.toml)

-cha, --channel-axis <channel_axis>

Coordinates shift axis.

Default:

0

Arguments

PATHS

Optional argument(s)

ultrack check_gurobi

ultrack check_gurobi [OPTIONS]

ultrack clear_database

Cleans database content.

ultrack clear_database [OPTIONS] {all|links|solutions}

Options

-cfg, --config <config>

Required Ultrack configuration file (.toml)

Arguments

MODE

Required argument

ultrack create_config

Creates a configuration file with default values.

ultrack create_config [OPTIONS] [OUTPUT_PATH]

Arguments

OUTPUT_PATH

Optional argument

ultrack data_summary

Prints a summary of the database data.

ultrack data_summary [OPTIONS]

Options

-cfg, --config <config>

Required Ultrack configuration file (.toml)

-o, --output-directory <output_directory>

Required Output plots directory.

Default:

summary

ultrack estimate_params

Helper command to estimate a few parameters from labeled data.

ultrack estimate_params [OPTIONS] [PATHS]...

Options

-r, --reader-plugin <reader_plugin>

Napari reader plugin.

Default:

napari

-l, --layer-key <layer_key>

Layer key to index multi-channel input.

Default:

0

-t, --timelapse, -nt

Indicates if data is a timelapse.

Default:

True

-o, --output-directory <output_directory>

Plots output directory

Default:

.

Arguments

PATHS

Optional argument(s)

ultrack export

Exports tracking and segmentation results to selected format.

ultrack export [OPTIONS] COMMAND [ARGS]...

ctc

Exports tracking results to cell-tracking challenge (http://celltrackingchallenge.net) format.

ultrack export ctc [OPTIONS]

Options

-o, --output-directory <output_directory>

Required Output directory to save segmentation and lineage graph (e.g. 01_RES).

-cfg, --config <config>

Required Ultrack configuration file (.toml)

-ow, --overwrite

Enables overwriting existing data.

-ma, --margin <margin>

Ignored margin on xy-plane.

Default:

0

-s, --scale <scale>

Output scale factor (e.g. 0.2,1,1 ). Useful when tracking was done on upscaled input.Must have length 3, first dimension is ignored on for 2-d images.

--first-frame-path <first_frame_path>

Optional first frame path used to select a subset of lineages connected to this reference annotations.

-di, --dilation-iters <dilation_iters>

Iterations of radius 1 morphological dilations on labels, applied after scaling.

Default:

0

--stitch-tracks

Stitches (connects) incomplete tracks nearby tracks on subsequent time point.

lp

Exports tracking ILP to .lp format.

ultrack export lp [OPTIONS]

Options

-o, --output-path <output_path>

Required ILP model (.lp) output path.

-cfg, --config <config>

Required Ultrack configuration file (.toml)

-ow, --overwrite

Enables overwriting existing data.

trackmate

Exports tracking results to TrackMate XML format.

ultrack export trackmate [OPTIONS]

Options

-o, --output-path <output_path>

Required TrackMate XML output path.

-cfg, --config <config>

Required Ultrack configuration file (.toml)

-ow, --overwrite

Enables overwriting existing data.

zarr-napari

Exports segments to zarr and tracks to napari tabular format (.csv for tracklets, parent relationship is lost).

ultrack export zarr-napari [OPTIONS]

Options

-o, --output-directory <output_directory>

Required Output directory to save segmentation masks and tracks table (e.g. results).

-cfg, --config <config>

Required Ultrack configuration file (.toml)

-ow, --overwrite

Enables overwriting existing data.

--measure

Add segmentation measurements to tracks table.

Default:

False

-i, --image-path <image_path>

If provided, tracks measurements will be enriched with intensity-based properties.

-r, --reader-plugin <reader_plugin>

Napari reader plugin.

Default:

napari

ultrack labels_to_contours

Converts and merges a sequence of labels into ultrack input format (foreground and contours)

ultrack labels_to_contours [OPTIONS] [PATHS]...

Options

-o, --output-directory <output_directory>

Required detection.zarr and contours.zarr output directory.

-r, --reader-plugin <reader_plugin>

Napari reader plugin.

Default:

napari

-s, --sigma <sigma>

Contour smoothing parameter (gaussian blur sigma). No blurring by default.

-ow, --overwrite

Enables overwriting existing data.

Arguments

PATHS

Optional argument(s)

ultrack segment

Compute candidate segments for tracking model from input data.

ultrack segment [OPTIONS] [PATHS]...

Options

-r, --reader-plugin <reader_plugin>

Napari reader plugin.

Default:

napari

-cfg, --config <config>

Required Ultrack configuration file (.toml)

-fl, --foreground-layer <foreground_layer>

Required Cell foreground layer index on napari.

-cl, --contours-layer <contours_layer>

Required Cell contours layer index on napari.

--insertion-throttle-rate <insertion_throttle_rate>

Rate at which to insert new hierarchies (group of competing segments) into the database.

-b, --batch-index <batch_index>

Batch index to process a subset of time points. ATTENTION: this it not the time index.

-ow, --overwrite

Enables overwriting existing data.

Arguments

PATHS

Optional argument(s)

ultrack solve

Compute tracks by selecting optimal linking between candidate segments.

ultrack solve [OPTIONS]

Options

-cfg, --config <config>

Required Ultrack configuration file (.toml)

-b, --batch-index <batch_index>

Batch index to process a subset of time points. ATTENTION: this it not the time index.

-ow, --overwrite

Enables overwriting existing data.

ultrack server

Start the websockets ultrack API.

ultrack server [OPTIONS]

Options

--host <host>

Host address

Default:

0.0.0.0

--port <port>

Port number to listen on

Default:

61234

--api-results-path <api_results_path>

Path to the API results folder

-cfg, --config <config>

Required Ultrack configuration file (.toml)