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:
- "Current file" (default option) will use the current root-file for the workspace (this is the file specified in the "Input control" module).
- "Matching format" will load the coordinate file matching a filename based on the root-file for the workspace and a series of rules.
- "Specific file" will load the coordinate file at the location specified by "Input file".
Name format (default = "Generic (from metadata)") Method to use for generation of the input filename:
- "Generic (from metadata)" (default) will generate a name from metadata values stored in the current workspace.
- "Input filename with prefix" will load a file with the same name as the input image, but with an additional prefix, specified by the "Prefix" parameter.
- "Input filename with suffix" will load a file with the same name as the input image, but with an additional suffix, specified by the "Suffix" parameter.
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:
- "From image" limits match the spatial and temporal dimensions of an image in the workspace (specified with the "Limits reference image" parameter). This is equivalent to how spatial limits are determined when identifying objects directly from an image.
- "Manual" limits are specified using the "Width", "Height", "Number of slices" and "Number of timepoints" parameters.
- "Maximum coordinate" limits are determined from the maximum x,y,z coordinates and timepoint present in the loaded coordinate set.
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:
- "From image" spatial calibrations match those of an image in the workspace (specified with the "Calibration reference image" parameter). This is equivalent to how calibrations are determined when identifying objects directly from an image.
- "Manual" spatial calibrations are specified using the "XY calibration (dist/px)" and "Z calibration (dist/px)" parameters.
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.