Plotting Histograms from Annotations

Use the Histogram tool to plot the intensity distribution within a region or along a ruler or path. Values can be extracted from any dataset available in the Data Properties and Settings panel.

Select the required ruler, path. or region in the Data Properties and Settings panel and then click the Histogram button in the Tools box to open the Histogram Analysis dialog, shown below.

Histogram Analysis dialog

Histogram options and measurements
	Description
Tools	The tools at the top of the dialog let you to pan, zoom, and reset the histogram, as well as save the figure and export the plotted values in the comma-separated values (*.csv extension) file format (see Histogram Tools).
Y log	If selected, the Y-axis will be plotted in log scale.
Bin count	Determines the interval in which values will be binned. Note It is especially important to specify the optimal bin size. Bins that are too wide can hide important details about distribution while bins that are too narrow can cause spikes just by coincidence.
Statistics*	Lets you select the statistics that will be computed. Selected statistics are shown on the histogram and can also be shown in the legend. 5th Percentile… Is the value below which 5% of the values in the distribution may be found. 95th Percentile… Is the value below which 95% of the values in the distribution may be found. Full Width Half Maximum… Is the width of the curve as measured between points on the Y-axis which are at the peak half maximum level. Mean… Indicates the mean intensity value within the distribution. Median… Indicates the median intensity value within the distribution. Minimum… Indicates the minimum intensity value within the distribution. Mode… Is the most commonly occurring value within the distribution. Standard Deviation… Indicates the standard deviation of intensity values. Shown as the range from the mean value on the histogram. Sum… Is the integral of all intensities of all of the pixels.
Dataset	Indicates the image data from which the values are extracted and provides a drop-down list for selecting other datasets.
Show legend	If selected, a legend with the selected measurements will be superimposed on the plotted values.
Copy to Clipboard	Copies the histogram statistics to the clipboard.

* Values are calculated for the selected image data and expressed in the native units of the dataset.

Histogram Tools

The Histogram tools allow you to pan and zoom, as well as reset the histogram.

Plotting tools
Item	Icon	Description
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 drawn rectangle, which can be defined by dragging your cursor over the area that you want to zoom.
Reset		Resets the original view of the figure.
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. *Standard image files (.jpeg, .jpg, .png, .tif, .tiff extensions)… Saves the histogram or profile as a bitmap image in the screen resolution. Postscript files (.eps, .ps extensions)… Saves the histogram or profile 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 histogram or profile in the Portable Graphics file format. The standard LaTeX picture environment can be used as a front end for PGF merely by using the `pgfpict2e` package. Requires the XeLaTeX compiler. Raw RGBA bitmap (.raw, .rgba extensions)… Saves the histogram or profile 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 histogram or profile 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 histogram or profile in the Adobe PDF file format.
Settings		Opens the Figure options dialog, shown below, in which you can select the plotted ranges, scaling, and labels for the axes. Edit the Min and Max values for each axis, as required. Edit the label of each axis, as required. Choose scaling — Log or Linear — for each axis, as required.
Export to CSV		Exports the plotted values in the comma-separated values (*.csv extension) file format.