Modules

Measure object intensity orientation

Calculates the orientation of structures in each object for a specific image.

Description

Calculates the orientation of structures in each object for a specific image. This module uses the Directionality_ plugin to calculate core measures. Additional measurements, such as the Alignment Index [1] are also calculated. All measurements are made for all slices within an object; that is, the individual slice histograms are merged and normalised prior to calculation of all measurements.

References:

  1. Sun, M., et al. "Rapid Quantification of 3D Collagen Fiber Alignment and Fiber Intersection Correlations with High Sensitivity" PLOS ONE (2015), doi: https://doi.org/10.1371/journal.pone.0131814

Parameters

ParameterDescription
Save locationSelect where the image should be saved.
  • "Mirrored directory" Save the image to a new directory structure which has the same layout as the input. This is useful when batch processing from a multi-layer folder structure. The subdirectory layout will match that of the input structure, but will have its root at the folder specified in "Mirrored directory root".
  • "Match Output Control" Save the image to the folder specified by the "Save location" parameter in "Output control".
  • "Save with input file" Save the image in the same file as the root file for this workspace (i.e. the image specified in "Input control".
  • "Specific location" Save the image to a specific folder.
Mirrored directory rootThe root path for the mirrored directory structure. This path is the equivalent of the folder specified in "Input control". All subfolders will be in the same relative locations to their input counterparts.
File pathPath to folder where images will be saved.
File name (generic)
Save name modeControls how saved image names will be generated.
  • "Match input file name" Use the same name as the root file for this workspace (i.e. the input file in "Input control".
  • "Specific name" Use a specific name for the output file. Care should be taken with this when working in batch mode as it's easy to continuously write over output images.
File nameFilename for saved image. Care should be taken with this when working in batch mode as it's easy to continuously write over output images.
Append series modeControls if any series information should be appended to the end of the filename. This is useful when working with multi-series files, as it should help prevent writing files from multiple runs with the same filename. Series numbers are prepended by "S". Choices are: None, Series name, Series number.
Append date/time modeControls under what conditions the time and date will be appended on to the end of the image filename. This can be used to prevent accidental over-writing of images from previous runs:
  • "Always" Always append the time and date on to the end of the filename.
  • "If file exists" Only append the time and date if the results file already exists.
  • "Never" Never append time and date (unless the file is open and unwritable).
Add filename suffixA custom suffix to be added to each filename.
Input image
Input objects
Method
Number of bins
Histogram start (°)
Histogram end (°)
Include bin range in name
Include number of bins in name
Save histogram
Histogram grouping
Parent objects name