Viewer Controls
Biom 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
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
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