Description

Load centroid coordinates of pre-detected objects from file. Loaded objects are stored in a single object collection and are represented by a single coordinate point. For example, this module could be used to import detections from another piece of software or from a previous analysis run.

Parameters

Output objects (default = "") Objects loaded into the workspace will be stored with this name. They will be accessible by subsequent modules using this name.

Coordinate source (default = "Current file") Controls where the coordinates for the output object collection will be loaded from:

Name format (default = "Generic (from metadata)") Method to use for generation of the input filename:

Generic format (default = "") Format for a generic filename. Plain text can be mixed with global variables or metadata values currently stored in the workspace. Global variables are specified using the "V{name}" notation, where "name" is the name of the variable to insert. Similarly, metadata values are specified with the "M{name}" notation.

Available metadata fields (default = "") List of the currently-available metadata values for this workspace. These can be used when compiling a generic filename.

Prefix (default = "") Prefix to use when generating coordinate file filename in "Input filename with prefix" mode.

Suffix (default = "") Suffix to use when generating coordinate file filename in "Input filename with suffix" mode.

Extension (default = "") Extension for the generated filename.

Include series number (default = "true") Option to include the current series number when compiling filenames. This may be necessary when working with multi-series files, as there will be multiple analyses completed for the same root file.

Input file (default = "") Path to specific file to be loaded when "Coordinate source" is in "Specific file" mode.

ID-column index (default = "0") Index of column in input coordinates file specifying the object ID number.

X-column index (default = "1") Index of column in input coordinates file specifying the object x-centroid location (pixel units).

Y-column index (default = "2") Index of column in input coordinates file specifying the object y-centroid location (pixel units).

Z-column index (default = "3") Index of column in input coordinates file specifying the object z-centroid location (slice units).

Timepoint-column index (default = "4") Index of column in input coordinates file specifying the timepoint the object appears in. Timepoint numbering starts at 0.

Limits source (default = "From image") Controls how the spatial limits (width, height, number of slices and number of timepoints) for the output object collection are defined:

Limits reference image (default = "") Image used to determine spatial and temporal limits of the output object collection if "Limits source" is set to "From image".

Width (default = "512") Output object collection spatial width to be used if "Limits source" is set to "Manual". Specified in pixel units.

Height (default = "512") Output object collection spatial height to be used if "Limits source" is set to "Manual". Specified in pixel units.

Number of slices (default = "1") Output object collection number of slices (depth) to be used if "Limits source" is set to "Manual". Specified in slice units.

Number of timepoints (default = "1") Output object collection number of frames to be used if "Limits source" is set to "Manual".

Calibration source (default = "From image") Controls how the spatial calibration for the output object collection are defined:

Calibration reference image (default = "") Image used to determine spatial calibrations of the output object collection if "Calibration source" is set to "From image".

XY calibration (dist/px) (default = "1.0") Distance per pixel in the XY plane. Units for this are specified in the main "Input control" module.

Z calibration (dist/px) (default = "1.0") Distance per slice (Z-axis). Units for this are specified in the main "Input control" module.

Create parent objects (default = "false") When selected, an output parent object collection can also be specified which allows objects to be linked. These parent objectcs can only perform a linking function for the output objects; the parent objects themselves do not contain any coordinate information. For example, the loaded parent objects could be tracks or clusters.

Parent objects type (default = "Normal") Controls the type of parent objects being used if the "Create parent objects" parameter is selected. Choices are: [Ljava.lang.String;@7dc0f706.
Output parent objects name (default = "") Name of the output parent objects collection.

Parent object ID index (default = "5") Index of column in input coordinates file specifying the parent object ID number.