Profiling Intensity

You can use the Intensity Profile function to profile the intensity values of image data along the length of a ruler or path. In Advanced Mode, you can plot multiple profiles from selected datasets.

Select a ruler or path in the Data Properties and Settings panel and then click the Profile button in the Tools box to open the Intensity Profile dialog, shown below.

Intensity Profile dialog

Intensity profile options and statistics
	Description
Annotation	Indicates the ruler or path along which the profile values will be extracted. You can select another ruler or path in the drop-down menu, if required. Length… Indicates the length of the selected ruler or path.
Dataset	When working in Standard mode, indicates the image data from which the profile values will be extracted. You can select another dataset in the drop-down menu, if required.
Number of points	Indicates the number of points that will be sampled when the profile is plotted. You can adjust the number of points, if required. Reset… Resets the number of points that will be sampled to maximum possible for the selected annotation and dataset(s), based on length and image spacing.
Averaging mode	Lets you average the probed intensity values within a disk or square perpendicular to the selected annotation. The diameter of disk or square can be set in the Diameter edit box. Point… Averaging will not be done. Disk… Averaging will done with a disk of a set diameter. Square… Averaging will done within a square of a set diameter.
Plot title	Indicates the title that appears above the profile. You can enter a new title for the profile in the Plot title edit box, if required.
Dataset selector	When working in Advanced mode, lets you select the dataset(s) from which the profile(s) will be plotted, as well as the data range displayed. By default, the profiles of all datasets available in the Properties and Settings panel are plotted.
Show statistics	If checked, describes the plotted values as follows: Minimum… Indicates the minimum value(s) within the selected dataset(s), as computed for the selected Averaging mode. Maximum… Indicates the maximum value(s) within the selected dataset(s), as computed for the selected Averaging mode. Mean… Indicates the mean value(s) within the selected dataset(s), as computed for the selected Averaging mode. Standard deviation… Indicates the standard deviation(s) of plotted values. Note Values are expressed in the native units of the dataset(s).
Y-axis scaling	When working in Advanced mode, lets you choose how Y-axis scaling will be applied. Scale to plotted datasets… If selected, the Y-axis will be scaled to the plotted datasets. Scale to selected range(s)… If selected, the Y-axis will be scaled to the range of the datasets selected in the Range column. Proportional multi-scale… If selected, the profiles will be scaled proportionally. Use this feature to compare the shapes of multiple profiles plotted from datasets saved in different data types.
Extra lines	Lets you add additional information to the graph. None… No additional information will appear on the graph. Global minimum, mean, and maximum… The minimum, mean, and maximum values, as computed for the selected Averaging mode and all plotted datasets, will be added to the graph. Individual minimum and maximum… The original minimum and maximum values will appear on the graph as a series of dotted lines in additional to the averaged values for each plotted dataset, which appear as a series of solid lines. Note The appearance of extra lines can be customized in the Figure Options dialog (see Profile Tools).
Advanced mode	If checked, the options for working in Advanced mode will be available (see Working in Advanced Mode).
Copy to clipboard	Copies the profile statistics to the clipboard.
Coordinates	The X-Y coordinates of the cursor position on the profile are indicated at the bottom of the dialog, as shown below.
Tools	Lets you zoom, pan, and reset the intensity profile. You can also save the figure as an image or other graphic type, as well as export profile data in the comma-separated values (*.csv extension) file format (see Profile Tools).

Whenever you plot an intensity profile, you can choose to work in Standard mode, in which case the plot of a single dataset will be available (see Working in Standard Mode), or you can choose to work in Advanced mode, in which case you can plot the profiles of multiple datasets (see Working in Advanced Mode).

Working in Advanced Mode

In Advanced mode, you can profile the intensity values of a selected ruler on multiple datasets.

Intensity Profile in Advanced mode

Select the required ruler or path in top section of the Data Properties and Settings panel.
Click the Profile button in the Tools box.
By default, the profile appears in the last-accessed mode.
Make sure that Use advanced mode is checked. This option is available at the bottom left of the dialog.
Enter a new title for the profile in the Plot title edit box, optional.
Select the ruler or path you need to profile in the drop-down list, if required.
Change the number of points that will be sampled, optional.
Note You change the number of points by entering a new value in the edit box or by clicking the Increase or Decrease buttons.
Select the datasets you want to be plotted in the Dataset Selector box.
By default, the profiles of all datasets available in the Properties and Settings panel are plotted.
Select the Y-axis scaling as follows:
Scale to all datasets… If selected, the Y-axis will be scaled to all datasets.
Scale to plotted datasets… If selected, the Y-axis will be scaled to the selected datasets.
Scale to SR datasets… If selected, the Y-axis will be scaled to the selected restricted (SR) datasets. You can select these datasets by checking the appropriate boxes in the SR column in the Dataset selector box.
Proportional multi-scale… If selected, the profiles will scaled proportionally. Use this feature to compare the shapes of multiple profiles.
Select the Show statistics option, optional. If checked, the minimum, maximum, mean, and standard deviation for each plotted dataset will appear in the Dataset selector box.
Adjust the view of the profile with the Pan and Zoom tools, as required.
You can also adjust the range of the X and Y axes and their associated labels, as well as the color and style of all curves and markers (see Profile Tools).
Save the profile data in a comma-separated values file, copy data to the clipboard, or create a bitmap image or scalable vector graphic of the histogram, optional (see Profile Tools).

Profile Tools

The Profile tools, shown below, let you pan and zoom profiles, customize the figure, as well as save profiles as bitmaps, vector graphics, or PDFs.

Profile tools

Profile tools and options
	Icon	Description
Log Y	-	If checked, the Y-axis of the profile will be plotted in Log scale.
Reset		Resets the original view of the figure.
Pan		Pans or zooms the figure as described below. Pan… Click with the left mouse button and then drag to pan the figure. Zoom on the Y axis… Click with the right mouse button and then drag up and down to Zoom in and Zoom out on the Y axis. Zoom on the X axis… Click with the right mouse button and then drag left and right to Zoom in and Zoom out on the X axis.
Zoom		Zooms to a selected rectangle, which can be defined by dragging your cursor over the area that you want to zoom.
Save		Saves the figure as a bitmap image, vector graphic, or in the PDF file format. The figure can also be saved as raw data or PGF code for LaTeX. *Standard image files (.jpeg, .jpg, .png, .tif, .tiff extensions)… Saves the figure as a bitmap image in the screen resolution. Postscript files (.eps, .ps extensions)… Saves the figure as an encapsulated postscript or postscript file. These types of files have a selectable resolution and provide high-quality graphics for publications. PGF code for LaTeX (.pgf extension)… Saves the figure in the Portable Graphics file format. Raw RGBA bitmap (.raw, .rgba extensions)… Saves the figure as a raw bitmap image file, in which the file contains only a list of pixel colors and nothing else. Scalable vector graphics (.svg, .svgz extensions)… Saves the figure in an XML-based vector image format. The SVG specification is an open standard developed by the World Wide Web Consortium (W3C). SVG images and their behaviors are defined in XML text files. Portable document format (.pdf extension)…* Saves the figure in the Adobe PDF file format.
Edit		Opens the Figure Options dialog, in which you can customize the appearance of the figure. The Figure Options dialog includes two tabs — Axes and Curves. Axes… Lets you modify the range of data shown on the X and Y axes, as well as their labels. Curves… Lets you modify the style, width, and color of the lines that appear on the figure, as well as any markers that are added to a line.
Export		Exports profile data in the comma-separated values (*.csv extension) file format.
Reset		Resets the figure.