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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 sagittal sliceAnalyze only the current sagittal slice
Current coronal sliceAnalyze only the current coronal slice
Current axial sliceAnalyze only the current axial slice
All slicesAnalyze the entire volume (default)

Histogram Display​

ControlDescription
Y-axisLinear or Logarithmic scale for the frequency axis
Graph typeBar, Line, or Filled line visualization style
Number of binsNumber of histogram bins (range: 10–100,000, default: 128)

Parameters​

Y-axis Scale​

OptionDescription
LinearStandard linear frequency scale
LogarithmicLogarithmic scale to better visualize low-frequency values

Graph Type​

OptionDescription
BarTraditional bar chart histogram
LineLine graph connecting bin values
Filled lineLine graph with filled area below

Number of Bins​

Controls the granularity of the histogram. More bins provide finer detail but may increase noise. Fewer bins show broader trends.

  • Minimum: 10 bins
  • Maximum: 100,000 bins
  • Default: 128 bins
tip

For most applications, 128-256 bins provides a good balance between detail and noise. Use logarithmic Y-axis scale when examining datasets with wide intensity ranges.

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 (sagittal, coronal, or axial)
  4. The histogram reflects only that slice's pixel values

Export​

Click the Export... button to save the histogram data to disk.

Export Options​

The histogram can be exported for external analysis or documentation purposes.

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