Load objects

Load centroid coordinates of pre-detected objects from file.

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

Parameter	Description
Output objects	Objects loaded into the workspace will be stored with this name. They will be accessible by subsequent modules using this name.
Coordinate source	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	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	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.
Prefix	Prefix to use when generating coordinate file filename in "Input filename with prefix" mode.
Suffix	Suffix to use when generating coordinate file filename in "Input filename with suffix" mode.
Extension	Extension for the generated filename.
Include series number	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	Path to specific file to be loaded when "Coordinate source" is in "Specific file" mode.
ID-column index	Index of column in input coordinates file specifying the object ID number.
X-column index	Index of column in input coordinates file specifying the object x-centroid location (pixel units).
Y-column index	Index of column in input coordinates file specifying the object y-centroid location (pixel units).
Z-column index	Index of column in input coordinates file specifying the object z-centroid location (slice units).
Timepoint-column index	Index of column in input coordinates file specifying the timepoint the object appears in. Timepoint numbering starts at 0.
Limits source	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	Image used to determine spatial and temporal limits of the output object collection if "Limits source" is set to "From image".
Width	Output object collection spatial width to be used if "Limits source" is set to "Manual". Specified in pixel units.
Height	Output object collection spatial height to be used if "Limits source" is set to "Manual". Specified in pixel units.
Number of slices	Output object collection number of slices (depth) to be used if "Limits source" is set to "Manual". Specified in slice units.
Number of timepoints	Output object collection number of frames to be used if "Limits source" is set to "Manual".
Frame interval	Time between adjacent frames if dealing with objects detected across multiple timepoints. Units for this are specified in the main "Input control" module.
Spatial calibration source	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 "Spatial calibration ref. 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.
Spatial calibration ref. image	Image used to determine spatial calibrations of the output object collection if "Spatial calibration source" is set to "From image".
XY calibration (dist/px)	Distance per pixel in the XY plane. Units for this are specified in the main "Input control" module.
Z calibration (dist/px)	Distance per slice (Z-axis). Units for this are specified in the main "Input control" module.
Temporal calibration source	Controls how the temporal calibration for the output object collection is defined: "From image" temporal calibration matches that of an image in the workspace (specified with the "Temporal calibration ref. image" parameter). This is equivalent to how calibrations are determined when identifying objects directly from an image. "Manual" temporal calibration is specified using the "Frame interval" parameter.
Temporal calibration ref. image	Image used to determine the temporal calibration of the output object collection if "Temporal calibration source" is set to "From image".
Create parent objects	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.
Output parent objects name	Name of the output parent objects collection.
Parent object ID index	Index of column in input coordinates file specifying the parent object ID number.