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: 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:

Name format: Method to use for generation of the input filename:

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:

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:

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:

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.