Color by Measurements

Measurements > Color By Measurements

Colors the separate features in the Current Image according to a set of feature measurements. The interface separates the measurement table, overlay visualization, and histogram into distinct panels with settings that can be saved and automatically applied during batch processing.

1. Top Toolbar

• Configure Report: Set up Report Generator options for Color By Measure visualizations.
• Other Batch Output: Configure automatic export of individual Color By Measure graphics during batch processing. The Batch Processor can generate CSV spreadsheets, PNG overlay images, and PNG histogram images for every processed image.
• Save Settings: Save all current visualization settings to the recipe for convenient recall and consistent batch processing. If Color By Measure is reached through the play button, these settings will be automatically used the next time Color By Measure is run and will apply to any automatically generated output graphics and reports.

2. Measurements Panel

The left panel displays a table of all feature measurements. The currently selected column in the Measurements table determines which measurement is visualized in the Overlay and plotted in the Histogram.

• Load: Load previously generated measurement files (.csv or .xlsx)
• Generate: Open the Feature Measurements dialog to select and calculate new measurements. Refer to Feature Measurements page for further description on each feature measurement
• Export: Export current measurements to spreadsheet format
• Show Highlighted Feature checkbox: Outlines the selected feature in the overlay
• Show on Histogram: Places a marker on the histogram for the selected feature
• Show Text Overlays: Displays measurement values directly on features. Click the Edit button (pencil) to change contents, style and position
• Show Text Overlays Settings (pencil button): Configure appearance and position of text overlays

• Content: Select to display the Feature ID number as well as desired measurements. See Include and Name
• Decimals: Specify the number of digits after the decimal point to include in the overlay
• Font Size: Specify the font size of the overlay
• Font Color: Specify the font color of the overlay
• Background Color: Specify the background color of the overlay or select ‘None’ for a transparent background
• Text Alignment: Specify the alignment to center, ‘left’ will move the elements to the right of center to left justify, ‘right’ will move the elements to the left of center to right justify and ‘center’ will center the text
• Position: Specify the overlay position relative to the feature bounding box. X and Y offset allow for the position to be fine-tuned
• Include: Select to include the element in the overlay
• Name: Select to include the element name in the overlay

3. Overlay Panel

The center panel shows features colored according to their measurement values with an integrated colorbar.

• Show Scale Bar: Toggle scale bar visibility and customization settings.
• Show Colorbar checkbox: Toggle colorbar visibility. Colorbar displays the full measurement range with automatic scaling
• ID: Enable to click features for identification. Click any feature to identify it in the measurements table.
• Unpreview: Reset the visualization
• Font size, Opacity, Limits, Colormap, and Opacity controls for fine-tuning the display
• Save Image: Save the colored overlay image

4. Histogram Panel

The right panel displays the distribution of the selected measurement with summary stats.

*Right-click on these stats and select “Copy” to copy them to the clipboard

• Show Image Name checkbox: Display the source image filename
• Bins: Auto-calculated or manually set the number of histogram bins. Click the ellipsis to set custom bin limits.
• Format: Font size, and X/Y axis limits can be manually adjusted for optimal visualization
• Curve Fit: Add Normal, Lognormal, or Bimodal distribution fits. See Curve Fitting for detailed information. Fit parameters are automatically extracted and can be included in reports.
• Fit Options: Access advanced curve fitting parameters and constraints
• Coloring: Choose histogram bar coloring – linked to colormap or single color
• Export: Export the bins vs. counts histogram data as a CSV file
• Save: Save the histogram plot as a high-resolution image