Image Adjustments

Core Feature

This feature is available in all MATISSE Explorer deployments.

Image adjustments allow you to modify the appearance of the background tissue image. Adjust opacity, brightness, contrast, and saturation to improve visibility or emphasize specific features.

TIP

Image adjustments are accessed through the Layer Settings popover. Click the Layers button (layer icon) in the map viewer toolbar, then find the Image layer section.

Automatic Image Mode Detection

MATISSE Explorer automatically detects the type of GeoTIFF image based on the number of bands:

Image Type	Band Count	Mode	Default Settings
RGB (H&E, brightfield)	3+ bands	Multi-band	Standard settings
Fluorescence (DAPI, etc.)	1 band	Single-band (grayscale)	Max Intensity: 2048, additional controls

When a single-band (grayscale) image is detected, additional controls appear automatically:

Max Intensity slider for contrast stretch
Channel Color selector for pseudocolor display

Available Adjustments

Opacity

Control the visibility of the background image.

Value	Effect
0	Completely hidden
1	Fully visible (default)

Use cases:

Lower opacity to make data points stand out
Hide completely for data-only views

Brightness

Control the overall lightness of the image.

Value	Effect
-1	Maximum darkening
0	Original brightness (default)
+1	Maximum brightening

Use cases:

Increase brightness for dark tissue images
Decrease brightness to reduce distraction from background

Contrast

Control the difference between light and dark areas.

Value	Effect
-1	Minimum contrast (flatter)
0	Original contrast (default)
+1	Maximum contrast (sharper)

Use cases:

Increase contrast to see tissue boundaries more clearly
Decrease contrast if image appears too harsh

Saturation

Control the intensity of colors in the image.

Value	Effect
-1	Grayscale (no color)
0	Original saturation (default)
+1	Maximum saturation (vivid)

Use cases:

Reduce saturation if tissue colors compete with data point colors
Grayscale mode helps data points stand out
Increase saturation to emphasize tissue staining

Max Intensity (Single-band (grayscale) only)

TIP

This control only appears for single-band (grayscale) images such as fluorescence microscopy.

Control the contrast stretch for fluorescence images. Lower values make the image brighter by mapping pixel values to a narrower range.

Value	Effect
1	Maximum brightness (may clip highlights)
2048	Default for fluorescence (good starting point)
65535	No contrast stretch (original 16-bit range)

Use cases:

Lower Max Intensity to brighten dark fluorescence images
Increase if image appears overexposed or washed out
Typical range for DAPI: 1000-5000

How it works:

Pixel values are divided by Max Intensity before display. For example:

A pixel with value 2000 at Max Intensity 2048 displays at ~98% brightness
The same pixel at Max Intensity 10000 displays at ~20% brightness

Channel Color (Single-band (grayscale) only)

TIP

This control only appears for single-band (grayscale) images such as fluorescence microscopy.

Apply pseudocolor to single-band (grayscale) images for better visualization.

Color	Common Use
Grayscale	Default, neutral display
Blue (DAPI)	Nuclear staining
Green (FITC)	Common fluorophore
Red (Cy3)	Common fluorophore
Cyan	Custom visualization
Magenta	Custom visualization
Yellow	Custom visualization

Use cases:

Match the display color to the actual fluorophore used
Improve visibility of specific features
Create publication-ready images with standard color conventions

Accessing Image Adjustments

Click the Layers button (layer icon) in the map viewer toolbar
In the popover, locate the Image layer section
Adjust sliders for opacity, brightness, contrast, and saturation
Changes apply immediately

TIP

The Image layer section only appears when the current projection mode includes a background image (e.g., Spatial view with tissue image).

Resetting Adjustments

Click the Reset button (rotate icon) in the Image layer section to restore all image settings to their defaults:

Standard defaults:

Opacity: 1
Brightness: 0
Contrast: 0
Saturation: 0

Additional defaults for single-band (grayscale) images:

Max Intensity: 2048
Channel Color: Grayscale

INFO

The image mode (single-band vs multi-band) is not reset. It is determined by the image file itself.

Recommended Settings

For H&E Stained Tissue

Standard histology images:

Brightness: 0 to +0.2
Contrast: 0 to +0.2
Saturation: -0.3 to 0

For Fluorescence Images

Single-band (grayscale) fluorescence images (automatically detected):

Max Intensity: 1000-5000 (adjust based on signal strength)
Channel Color: Match to fluorophore (e.g., Blue for DAPI)
Brightness: 0 (use Max Intensity instead)
Contrast: 0 to +0.2
Saturation: 0 (not applicable for pseudocolor)

For Data Focus

When data points are the priority:

Opacity: 0.3 to 0.7
Brightness: -0.2 to 0
Contrast: -0.2 to 0
Saturation: -0.5 to -1 (grayscale)

For Presentation

Clean, professional look:

Brightness: 0 to +0.1
Contrast: +0.1 to +0.2
Saturation: -0.2 to 0