Image Settings
Overview
Image viewer settings control visual properties like contrast limits, brightness, contrast, gamma, color maps, scalebars, and annotation overlays. All settings are accessed from the Selection panel on the right sidebar when an Image Viewer panel is selected.
Image Adjustments
The Image Adjustments section provides non-destructive contrast limits, brightness, contrast, and gamma controls for each Image Viewer panel.
| Control | Range | Default | Effect |
|---|---|---|---|
| Contrast Low | Any number | Auto (data min) | Sets the black point - pixel values at or below this are rendered black |
| Contrast High | Any number | Auto (data max) | Sets the white point - pixel values at or above this are rendered white |
| Brightness | −100 to +100 | 0 | Linear shift of pixel values (brighter or darker) |
| Contrast | −100 to +100 | 0 | Stretches or compresses values around the midpoint |
| Gamma | 0.1 to 5.0 | 1.0 | Power-curve correction (< 1 brightens shadows, > 1 darkens them) |
Contrast Low and High use number-only inputs. Clear the field to return to automatic (data-driven) range. Brightness, contrast, and gamma each use a combined number input and slider.
Processing pipeline
Adjustments are applied per-pixel in the following order:
- Contrast Limits - Pixel values are normalized using the Low/High range instead of the data min/max
- Contrast - Stretch or compress around 0.5
- Brightness - Linear offset
- Gamma - Power curve (clamped to 0–1 before exponentiation)
The processing factors are precomputed outside the pixel loop for performance.
Adjustments are purely visual and per-panel. The original data is never modified.
Dataset Defaults
A Dataset Defaults button appears whenever any adjustment differs from its initial state. Clicking it restores the panel to the state it was in when the dataset was first loaded:
- Files with embedded display metadata (e.g., DM3/DM4 from Gatan DigitalMicrograph): restores the file’s original brightness, contrast, gamma, and contrast limit values.
- Files without display metadata: resets to Nexus neutral values (brightness 0, contrast 0, gamma 1.0, auto contrast limits).
Dataset Defaults always returns to the initial load state - you never need to remember whether the file had embedded settings or not.
Multi-Frame Adjustments (2Dts Image Series)
For multi-frame signals (2Dts), the Image Adjustments section includes an Apply to dropdown with two scopes:
| Scope | Label | Effect |
|---|---|---|
| Parent | All Frames | Changes apply to every frame in the series |
| Frame | Current Frame | Changes apply only to the currently displayed frame |
The default scope is All Frames. When set to Current Frame, a blue dot (●) appears next to each slider label where the per-frame override value actually differs from the parent value.
Scope-aware buttons
| Scope | Button | Effect |
|---|---|---|
| All Frames | Dataset Defaults | Restores all frames to the initial load state (file metadata or Nexus neutral) and clears per-frame overrides |
| Current Frame | Reset Frame | Removes the per-frame override so the frame inherits the parent setting |
| Current Frame | Frame Dataset Defaults | Sets the current frame’s override to its per-frame metadata from the file |
The “Current Frame” option in the dropdown shows a dot (●) when the displayed frame has a per-frame override that differs from the parent, making it easy to spot customised frames.
Color Maps
The color map (or color scale) controls how pixel intensities are mapped to colors. Select from the drop-down in the Display Options section.
| Color Map | Description |
|---|---|
| Grayscale | Black to white (default) |
| Viridis | Perceptually uniform, blue → green → yellow |
| Plasma | Perceptually uniform, blue → red → yellow |
| Inferno | Perceptually uniform, black → red → yellow |
| Magma | Perceptually uniform, black → magenta → yellow |
| Jet | Classic rainbow (blue → cyan → green → yellow → red) |
| Turbo | Improved rainbow with better perceptual uniformity |
DM3/DM4 files with a stored CLUT (Color Look-Up Table) name are automatically mapped to the closest Nexus color map - for example, Gatan’s “Temperature” maps to Inferno, and “Rainbow” maps to Jet.
Scalebar Configuration
The scalebar is drawn automatically when the signal has spatial axis metadata. There is no manual toggle - it appears whenever sufficient axis information is available and is hidden otherwise.
Position and sizing
The scalebar is anchored to the bottom-right corner of the visible image area, with 20 px of padding from the edges. Its width is approximately 150 pixels at the current zoom level, and the label shows the exact physical length.
Automatic contrast
The scalebar samples the pixel brightness behind it and switches between white (on dark backgrounds) and black (on bright backgrounds) so that it stays readable on any image.
Scale values
The displayed length is chosen from a series of round values - 1, 2, 5, 10, 20, 50, 100, 200, 500, 1000, … - so the bar is easy to read at a glance.
Supported units
| Category | Units recognised |
|---|---|
| Real-space | m, µm, nm, pm, Å |
| Reciprocal-space | 1/nm, 1/Å, 1/m |
Real-space values are automatically converted to the most readable unit (for example, 1500 nm is shown as 1.5 µm). Reciprocal-space values are displayed with their original unit.
Signal Overlay
Draws a second 2D or 2Dts signal on top of the panel’s own signal - a mask, a script output, or another detector channel over a survey image. Controls are in the Signal Overlay section.
| Control | Options | Default | Effect |
|---|---|---|---|
| Overlay Signal | None, or any 2D / 2Dts signal | None | Which signal to draw on top. The panel’s own signal is excluded from the list |
| Opacity | 0-100% | 50% | How strongly the overlay covers the base image |
| Color Scale | Same seven maps as above | Viridis | Color map for the overlay, independent of the base image |
| Blend Mode | Normal, Color (tint base), Additive (Screen), Multiply | Normal | How overlay pixels combine with the image beneath |
| Transparent Zero | On / Off | Off | Renders pixels whose value is exactly zero fully transparent |
The remaining controls appear only once an overlay signal is selected.
Normalization
The overlay is normalized across its own min/max and colored with its own color map. It deliberately does not inherit the base image’s contrast limits - an overlay is usually a different measurement on a different scale, and reusing the base limits would typically render it entirely black or entirely saturated.
Blend modes
| Mode | Canvas operation | Use for |
|---|---|---|
| Normal | source-over |
Straight alpha blend |
| Color (tint base) | color |
Colouring the image while keeping its detail — usually what you want |
| Additive (Screen) | screen |
Brightening a signal over a dark image |
| Multiply | multiply |
Darkening, e.g. shading a region |
Color takes hue and saturation from the overlay and luminosity from the image beneath, so the base keeps its brightness and texture and is simply tinted. The other modes substitute the overlay’s own brightness, which suppresses the detail underneath: on a textured greyscale image, Normal at full opacity roughly halves the mean brightness and measurably flattens the texture, where Color leaves both unchanged.
Transparent Zero
Tests the raw data value, not the normalized one, so “zero” means zero in the data regardless of where the color range starts. The comparison is exact - values merely close to zero are still drawn.
Switch this on for masks and thresholded script outputs. With it off, the zero-valued background is drawn in the color map’s lowest color and covers the image underneath.
Positioning and scale
Overlay placement uses the spatial axis metadata of both signals: the pixel offset is (overlayAxisOffset - baseAxisOffset) / baseAxisScale, and the drawn size is scaled by the ratio of their axis scales. A cropped or differently-sampled overlay therefore lands in the right place within the base image. If either signal has no spatial axes, the overlay is drawn from the top-left at the base image’s scale.
Frame following
A 2Dts overlay follows the timeline together with the base image. If it has fewer frames than the base signal, it holds on its last frame rather than blanking.
Zoom & Pan Sync
Sync Zoom & Pan (in the Frame Navigation section) puts a panel into a shared viewport group. Every Image Viewer with the toggle on shares one zoom level and pan position, and driving any of them - mouse wheel, zoom buttons, fit-to-window, or drag-panning - moves all the others.
- Switching it on snaps the panel to the group’s current view.
- Switching it off leaves the panel where it is; it simply stops following.
- Panels that never had it on are unaffected.
- The toggle is saved with the project; the shared viewport itself is session state and is not persisted.
Synced panels match the zoom factor, not the physical field of view, and pan is shared as a screen-pixel offset. Two signals with different pixel sizes will therefore cover different physical areas at the same zoom, and panels of different sizes will not frame exactly the same region.
Annotation Overlay Settings
Annotation overlays show live signal values on top of the image. They are created by dragging a 0Dts signal onto an existing Image Viewer panel (see Image & Video Viewer → Annotations Overlay).
Display toggles
Two toggles are available in the panel settings:
| Setting | Default | Effect |
|---|---|---|
| Annotations | On | Show or hide all annotation badges |
| Annotation Labels | On | Show or hide signal names inside each badge (value and unit are still visible) |
Visual styling
Each annotation badge uses the signal’s workspace colour as a left-side accent border. The background is a semi-transparent version of the same colour with a backdrop blur for readability. Text is white.
Value formatting
Values are displayed with automatic decimal precision based on the data range - large values show fewer decimals, small values show more. Signal names longer than 20 characters are truncated, and camelCase names are converted to title case.
Removing an annotation
Hover over the panel and click the × button on the annotation badge. The signal is only removed from this panel - it stays in the workspace.