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Histogram

The Histogram tool generates a histogram visualization of grayscale values from the active volume dataset. This tool helps analyze the distribution of pixel intensities, which is useful for understanding image characteristics, setting thresholds, and quality assessment.

Accessing the Tool​

  1. Navigate to the Measure tab in the ribbon
  2. Click the Histogram button in the Measurement tools section
Prerequisites
  • An active volume dataset must be loaded in the project
  • Optionally, masks can be used to filter the analysis region

User Interface​

Description​

Displays: "Generate a histogram of the grayscale values from the active volume dataset, with the option to filter by the active mask or the union of visible masks. The histogram can be generated for either the entire volume or the current slice."

Options​

ControlDescription
TargetSelect the data source for histogram generation
SliceChoose which slice(s) to analyze

Target Options​

OptionDescription
Active volumeGenerate a histogram of all pixels in the active volume dataset
Active maskGenerate a histogram of pixels in the active volume that are within the active mask
Visible masksGenerate a histogram of pixels within the union of all visible masks

Slice Options​

OptionDescription
Current Plane 1 (YZ) sliceAnalyze only the current Plane 1 (YZ) slice
Current Plane 2 (XZ) sliceAnalyze only the current Plane 2 (XZ) slice
Current Plane 3 (XY) sliceAnalyze only the current Plane 3 (XY) slice
All slicesAnalyze the entire volume (default)

Histogram Chart​

The histogram is drawn in the Interactive Histogram Chart. Right-click the chart to reach its display options, its interval actions, and its export actions. The most used ones are listed below.

SettingDescription
ScaleLinear or logarithmic frequency axis
GraphBars, line, or filled line
BinningGroups the bins before they are drawn

The chart can be zoomed and scrolled, and a dragged range reports its mean, standard deviation, and share of the analyzed data. See the chart page for the full description.

Histogram Resolution​

The histogram is computed over 4096 bins across the gray value range of the volume. The chart groups them into 256 bins for display, which keeps the shape readable without hiding the measured resolution.

Use Binning in the chart context menu to change the grouping. Setting it to Off shows all 4096 computed bins, and Bin Count groups them into a number you choose. Regrouping only changes the drawing and the reported interval values, never the measured data, so it is immediate and can be changed as often as needed.

tip

Use the logarithmic scale when a single peak dominates the range, so the rare gray values next to it stay visible.

The same gray value distribution drawn with 256 bins, with 32 bins, and with 256 bins on a logarithmic frequency axis that keeps a small second peak visible

Workflow​

Basic Histogram Generation​

  1. Ensure a volume dataset is active
  2. Open the Histogram tool
  3. Select Active volume as the target
  4. Choose All slices to analyze the complete volume
  5. Adjust the number of bins if needed
  6. The histogram updates automatically

Masked Region Analysis​

  1. Create or activate a mask covering the region of interest
  2. Open the Histogram tool
  3. Select Active mask as the target
  4. The histogram shows only pixel values within the mask

Slice-Specific Analysis​

  1. Navigate to the slice of interest using the slice views
  2. Open the Histogram tool
  3. Select the corresponding slice option (Plane 1 (YZ), Plane 2 (XZ), or Plane 3 (XY))
  4. The histogram reflects only that slice's pixel values

Export​

Click the Export... button to save results. Export options include:

  • CSV file: Volume, mask, and slice information, followed by the histogram at its full resolution
  • PDF Report: The information, the histogram picture, and the histogram data table

The histogram picture in the report always shows the whole gray value range, so a zoom you set on screen does not change it. The histogram data table groups the gray values into as many rows as the chart draws bars, so that it fits into the report. Each row states the gray value range it covers, in a Grayvalue from and a Grayvalue to column, and the pixel count next to it is the exact number of pixels within that range.

The histogram in the CSV file and the Export as CSV... action in the chart context menu are both written at the full resolution of the analyzed region, not at the resolution the chart is drawn with. For an integer image this resolves every gray value, so each row carries one gray value and its pixel count. A floating point image has no gray value step, so each row covers a range of gray values and states it in a Grayvalue from and a Grayvalue to column. The chart can also be saved as a picture from the same menu; see Exporting the Chart.

If the active volume changes while the file dialog is open, the histogram can no longer be recomputed for the volume the chart shows. The export is then cancelled with a message instead of writing a file.

Interpretation​

Common Histogram Patterns​

PatternDescription
Single peakUniform tissue type or material
BimodalTwo distinct tissue types (e.g., bone and soft tissue)
Wide distributionHigh variation in intensity values
Narrow distributionHomogeneous region
Long tailPresence of outliers or noise

Medical Imaging Context​

For CT data, the X-axis represents Hounsfield Units (HU):

  • Air: approximately -1000 HU
  • Fat: -100 to -50 HU
  • Water: 0 HU
  • Soft tissue: 20–80 HU
  • Bone: 300–3000 HU
PageDescription
Interactive Histogram ChartReading, navigating, and evaluating the histogram chart
Volume StatisticsDetailed statistical analysis with tabular output
Draw Profile LineVisualize intensity along a line
Mask StatisticsStatistics for masked regions