> ## Documentation Index > Fetch the complete documentation index at: https://docs.biom.science/llms.txt > Use this file to discover all available pages before exploring further. # Viewer Controls > Image adjustments, channel controls, navigation, and toolbar tools. # Viewer Controls Relay provides a rich set of viewer controls tailored to the type of file you're viewing. Each pane has fully isolated viewport state, so adjustments in one pane don't affect others. ## Image adjustments These controls are available for all image types in two tabs: ### Basic tab | Control | Range | Description | | --------------------- | ------------------ | ------------------------------------------------- | | **Brightness** | 0–100 | Adjust overall image brightness (50 = neutral) | | **Contrast** | 0–100 | Adjust image contrast (50 = neutral) | | **Gamma** | 1–500% | Non-linear brightness correction (100% = neutral) | | **Saturation** | 0–200% | Color saturation (100% = neutral) | | **Hue** | -180 to +180 | Hue rotation (0 = neutral) | | **Threshold** | 0–255 | Binary threshold cutoff | | **Posterize** | 2–256 | Reduce color levels | | **Invert** | Toggle | Invert image colors | | **Remove Background** | Toggle + threshold | Subtract background with configurable threshold | | **Auto Threshold** | Button | Automatically calculate optimal threshold | | **Reset** | Button | Restore all adjustments to defaults | ### Color tab | Control | Range | Description | | ----------------- | ------------ | -------------------- | | **Red Balance** | -100 to +100 | Adjust red channel | | **Green Balance** | -100 to +100 | Adjust green channel | | **Blue Balance** | -100 to +100 | Adjust blue channel | ## Channel controls (scientific images) For multi-channel images (OME-TIFF, Zarr), the scientific controls panel provides per-channel editing: * **Visibility toggle** — eye icon to show/hide individual channels * **Color picker** — click the color swatch to assign a LUT color to any channel * **Intensity histogram** — interactive SVG histogram with draggable min/max handles for display range * **Gamma handle** — optional mid-tone adjustment on the histogram * **Auto-contrast** — automatically calculate p1/p99 percentile display range per channel from real histogram data * **Channel split mode** — split channels across separate panes, each showing one channel The histogram supports 8-bit (256 bins) and 12-bit (4096 bins) data, with log-scale display and pointer/keyboard navigation. ### Image metadata A collapsible metadata section shows: * Dimensions (width x height x channels x Z-slices x time-points) * Bit depth, file size, format * Pixel scale / physical size (used for scale bar) ## Navigation ### Z-stack navigation For multi-plane images: * **Z-slice slider** with debounced scrubbing (100ms) * **Play/pause animation** with configurable FPS (default 2 FPS) * **Step forward/backward** buttons * **Open in 3D** button — splits a new pane and loads the same image in the volume viewer * **Z-stack export** — export selected Z-range ### Time-series navigation For time-lapse images, use the time slider to scrub through time points. ### Keyboard navigation * **Arrow keys** — advance Z-slice or time-point * **Shift + Arrow keys** — advance by 10 steps * **Delete / Backspace** — delete selected annotation or clear loaded image ### Camera controls * **Pan** — click and drag with the hand tool, or hold middle mouse button * **Zoom** — scroll wheel, or use the zoom buttons in the toolbar * **Fit to view** — double-click the zoom controls to fit the image to the pane * **Camera linking** — link pan/zoom across multiple panes so they move in sync. Click the link icon in the pane header. ### Minimap A bird's-eye overview of the full image with a viewport rectangle. Click to navigate. Toggle via right-click context menu or the minimap icon. Setting persists per-pane. ### Scale bar Toggle the scale bar overlay for images with physical pixel size metadata. Shows in the bottom-right corner. ## Image layers (multi-image overlay) Overlay multiple images in a single pane by holding **Alt** while dropping a file: * Up to **8 image layers** per pane * Per-layer controls: **opacity** (0–100%), **visibility** toggle, **blend mode**, z-order * Reorder layers with move-up/move-down buttons * Each layer has independent channel overrides * Focus a layer to make it the active editing target The Image Layer panel appears in the sidebar when a pane has 2+ layers. ## Toolbar tools | Tool | Shortcut | Description | | ------------- | -------- | -------------------------------------------------------- | | **Select** | V | Select and move objects on the canvas | | **Pan** | H | Pan the view by clicking and dragging | | **Rectangle** | — | Draw rectangle shapes or regions | | **Circle** | — | Draw circle shapes or regions | | **Line** | — | Draw line shapes | | **Text** | T | Add text annotations | | **Pen** | — | Freehand drawing on the canvas | | **Comment** | — | Place comments at specific locations | | **SAM Point** | — | Click to segment with SAM (foreground/background points) | | **SAM Box** | — | Draw a bounding box to segment with SAM | ### Region selection tools | Tool | Shortcut | Description | | -------------------- | -------- | ------------------------------------------ | | **Rectangle Select** | Q | Select a rectangular region for processing | | **Circle Select** | W | Select a circular region | | **Lasso Select** | E | Freehand region selection | | **Polygon Select** | Y | Point-by-point polygon selection | ### Context menu (right-click) * **Add Image to Deck** — capture the current viewport as a card * **Show Minimap** — toggle the bird's-eye overview ## Volume 3D viewer When viewing Z-stacks, click **Open in 3D** to open the volume renderer in a new pane: | Control | Options | Description | | ----------------- | ------------------------------------- | ------------------------------------------------------ | | **Render Mode** | Volume / MIP / Isosurface | Rendering algorithm | | **Color Map** | Transfer function presets | Color mapping for intensity values | | **Opacity** | 0–100% | Volume opacity | | **Brightness** | 0.1–3x | Volume brightness multiplier | | **Iso Threshold** | 0–255 | Isosurface extraction threshold (Isosurface mode only) | | **Quality** | Low (128) / Medium (256) / High (512) | Number of ray-marching steps | | **Ortho Views** | Toggle | Show XY/XZ/YZ cross-section panels | | **Clip Planes** | X/Y range sliders | Clip the volume in X and Y (0–100%) | ## DICOM-specific controls When viewing DICOM files, adjustments map to DICOM-standard window/level: * **Window/Level presets** — dropdown with anatomy presets (Lung, Bone, Brain, etc.) * **Brightness = Window Center** / **Contrast = Window Width** * **Series selector** — switch between DICOM series in multi-series studies * **DICOM invert** — toggle MONOCHROME1/MONOCHROME2 * Supports both single files and multi-slice folders ## Video playback controls When viewing video files: * **Play/Pause** — start or stop playback * **Skip** — jump forward or backward * **Frame slider** — scrub to any frame * **Speed selector** — adjust playback speed * **Frame counter** — current frame number display * Videos auto-pause when you select an annotation tool, so you can annotate individual frames ## Spike viewer controls For electrophysiology data (NWB, H5, SpikeGLX .bin+.meta files): * **Waveform viewer** — extracted spike waveforms * **Power spectrum** — frequency domain analysis * **Detail channel** — zoomed view of individual channels * **Amplitude scatter** — spike amplitude distributions * **Correlogram** — cross-correlogram between units * **ISI histogram** — inter-spike interval distribution (linear or log scale) * **Template viewer** — average waveform templates per unit * **Sorting tabs** — view and navigate sorting results