Image Adjustments

Core Feature

This feature is available in all Portrai 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

Portrai 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)	Auto-detected contrast limits, additional controls

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

Contrast Limits range slider (Min/Max) 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

Contrast Limits (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 using a two-handle Min/Max range slider. This is the industry standard approach used by ImageJ, napari, QuPath, and other microscopy viewers.

Portrai Explorer automatically computes optimal contrast limits by analyzing the image data. The 0.05th and 99.95th percentiles of non-zero pixel values are used as initial Min/Max, ensuring the display range matches the actual signal distribution.

Handle	Default	Effect
Min	Auto-detected	Pixels at or below this value become black/transparent
Max	Auto-detected	Pixels at or above this value become full brightness

Use cases:

Raise Min to remove background noise and autofluorescence
Lower Max to brighten dim signals
Typical range for DAPI: Min 100–500, Max 1000–5000

How it works:

Pixel values are linearly mapped from the [Min, Max] range to [0, 1] for display:

display = clamp((pixel - min) / (max - min), 0, 1)

A pixel with value 500 at Min=100, Max=2000 displays at ~21% brightness
The same pixel at Min=0, Max=500 displays at 100% 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

Multi-Image Overlay

When a project contains multiple images (e.g., DAPI + Cell Boundary staining), Portrai Explorer automatically enables multi-image overlay mode:

Fluorescence channels are composited using additive blending — each channel is assigned a distinct pseudocolor and their signals are summed
H&E images (if present) render as the base layer, with fluorescence overlaid on top
Each channel has independent controls for color, contrast limits, opacity, and visibility
Pixels with no signal are transparent, allowing underlying layers to show through

See Layer Settings - Multi-Image Mode for detailed controls.

Accessing Image Adjustments

Click the Layers button (layer icon) in the map viewer toolbar
In the popover, locate the Image section
For multi-image mode: adjust per-channel settings
For single-image mode: adjust sliders for opacity, brightness, contrast, and saturation
Changes apply immediately

TIP

The Image 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:

Contrast Limits: Auto-detected from image data (percentile-based)
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):

Contrast Limits: Auto-detected; fine-tune if needed based on signal strength
Channel Color: Match to fluorophore (e.g., Blue for DAPI)
Brightness: 0 (use Contrast Limits 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