Preferences¶

The Preferences dialog lets you customize Microscopy Image Browser to suit your workflow, from interface appearance to tool behavior and external integrations.
Open it via Ribbon → Home → Preferences.
Settings are grouped into categories, accessible through a tree on the left, making it easy to tweak everything from fonts to undo history.

Overview¶

The dialog organizes settings into seven categories, shown as nodes in the Categories Tree on the left side:

• User interface: controls fonts, GUI scaling, mouse actions, and update checks settings.
• Colors and styles: sets colors for models, masks, annotations, and contour styles.
• Backup and undo: configures undo history for 2D and 3D operations.
• External directories: specifies paths for external tools like Fiji or Python.
• Keyboard shortcuts: defines custom key bindings for MIB actions.
• Segmentation tools: adjusts settings and options for segmentation tools.
• Input / output: selects the OME-Zarr (zarr3) read/write engine, the zarr chunk cache size, and BigData label smoothing.

At the bottom, you’ll find buttons to manage changes:

• Help: opens help documentation for the Preferences dialog.
• Default: restores all settings to their original values.
• OK: saves changes and closes the dialog.
• Apply: saves changes without closing.
• Cancel: discards changes and closes.

Use the Categories Tree to switch between panels. Click a node (e.g., User interface) to show its settings. Changes are saved only when you click OK or Apply.

User Interface¶

This category customizes how MIB’s interface looks and behaves, covering fonts, scaling, mouse interactions, and update frequency.

GUI Tweaks¶

Fine-tune how the mouse and rendering work:

Mouse wheel action: a dropdown to set the mouse wheel’s function:

• Zoom In/Out: zooms the image.
• Change slices/frames: switches between slices or time frames (default).
  

Left mouse action: a dropdown to assign the left mouse button’s role:

• Pan image: Moves the image.
• Selection/drawing: Enables drawing and segmentation (default).

Image resize method: a dropdown to choose how images are interpolated for visualization in the Image Document:

• auto: uses nearest for >100% zoom, bicubic for <100% (default).
• nearest: fastest, lower quality.
• bicubic: slowest, highest quality.
  

Enable selection: a dropdown to toggle existence of the Selection layer:

• yes: Enables segmentation tools (default).
• no: Saves memory but disables segmentation.

This setting is applied to the currently shown dataset and to every dataset loaded afterwards. It does not affect the empty placeholder datasets that MIB creates at startup and when a dataset is closed: those always keep the Selection layer, so the brush and the other segmentation tools can be tried on the default image right away.

Number of recent dirs: a numeric field to set how many recently accessed directories MIB remembers.

3D rendering engine: a dropdown to select the engine for 3D visualization:

• Viewer3d, R2022b: Modern engine, available in R2022b or newer version of MATLAB (default).
• Volshow, R2018b: Legacy engine, available in R2018b or newer .
  

Hold Alt with Scroll Wheel: a dropdown to define behavior when holding Alt while scrolling :

• Return to the slice: returns to the current slice upon release of Alt (default)
• Scroll time points: Alt + mouse wheel scrolls through time points.

Update Check¶

Set how often MIB looks for a new version:

Recheck for update, days: a numeric field (minimum 1) to define the interval between update checks (default: 30 days).

Font¶

Adjust the font used across MIB interface:

• Select font...: a button that opens a font selection dialog. The chosen font is displayed in the Current Font label field below.
• Font size: a numeric field (minimum 1) to set the font size for GUI widgets, like buttons and labels.
• Font size for directory contents: a numeric field (minimum 1) to set the font size for the file list in the Directory Contents Panel.

Parallel Processing¶

Number of CPUs: a numeric field to set the maximum number of CPU cores used for parallel processing operations. Reducing this value frees CPU resources for other applications running on the same workstation.

GUI Scaling¶

Scale MIB’s interface, useful for high-DPI screens or accessibility:

OS Scaling Factor: a numeric field to input the operating system’s scaling factor (as ratio vs 100%), ensuring accurate mouse coordinates.

MIB Scaling Factor: a numeric field to scale selected GUI elements, such as panels or tables specified as a ratio relative to default size.

It is possible to configure each element specifically as on some MacOS versions the scaling needs to be done excluding some widgets.

• uipanel: scales panel containers.
• uitab: scales tab elements.
• uitable`: scales tables.
• uibuttongroup: scales button groups.
• uitabgroup: scales tab groups.
• axes: scales axis displays.
• uicontrol: scales other control elements like buttons.

Rescale GUI: press the button to instantly apply scaling changes to MIB’s main window.

Colors and Styles¶

This category lets you customize colors for materials of the model, color channels, layers, and contours, as well as rendering styles.

Palette generator¶

Generate color palettes from several predefined presets for visualization of materials within the Segmentation table.

• Palette generator: a dropdown to pick predefined color palettes for the tables.
• Number of colors: a dropdown to set the number of colors in the generated palette, depending on the selected preset.

Colors of the materials table¶

The table shows the colors of materials that define visualization of the model. The colors can be changed by typing intensity value for each Red, Green, Blue channels in range from 0-1 or 0-255 (depending on scale to 0-1) or by the colored cells.

• Reverse colormap: press to reverse the order of colors in the palette
• Insert color: insert a new random color at the following row in the table
• Replace with random color: replace the selected color with a random color
• Swap two colors: swap the selected color with another one
• Delete color(s): delete selected color from the palette
• Import (from MATLAB or file): import a palette from the main MATLAB workspace or from a file
• Export (to MATLAB or file): export the current palette to the main MATLAB workspace or to a file

scale to 0-1: a checkbox to normalize colors between 0 and 1, otherwise the colors are scaled between 0 and 255.

Colors for LUT and image layers¶

LUT Colors for Color Channels - is a table with columns for Red, Green, Blue, and a Preview, used for definition of LUT (Look Up Table) colors to visualize individual color channels of the dataset.

The LUT color channel is also available from the View Settings panel. Whenever LUT is checked in the View Settings->LUT table these colors are used.

Selection: a button to specify color to be used for rendering of the Selection layer
Mask: a button to specify color to be used for rendering of the Mask layer
Annotations a button to specify color to be used for rendering of annotations
cursor matching selected material: when checked, the brush cursor takes the color of the material or Mask it paints into; otherwise it stays dark green

Contours¶

Adjust how contours are drawn for models and masks:

Rendering: a dropdown for contour rendering method:

• quality: high-quality rendering (default).
• performance: faster, but touching objects use the earlier material’s color.

Model thickness: a numeric field for line thickness in Contour mode for models (default: 1).
Mask thickness: a numeric field for line thickness in Contour mode for masks (default: 1).

Mask method: a dropdown for Mask contour direction:

• inwards: Shrinks the mask object (default).
• outwards: Grows the mask object.

Labels¶

Control Labels layer appearance:
show as contours: show the Labels layer as filled shapes (default)
show as contours: show the Labels layer as contours instead of filled shapes

Masks¶

Control Mask layer appearance:
show as contours: show the Mask layer as contours instead of filled shapes (default)
show as contours show the mask as filled shape

Backup and Undo¶

Configure undo functionality for editing operations:

enable undo: a checkbox to turn on undo support.

Number of history steps to store: a numeric field (minimum 0) for the total number of 2D and 3D operations to store. Higher values save more steps but use more memory. Number of 3D history steps to store: a numeric field (minimum 0) for 3D operations only. Must be smaller than the total history steps.

External Directories¶

Specify paths for external tools and packages that integrate with MIB. Leave fields empty if you don’t use a particular package.

Bioformats Memoizer temporary directory: a text field and ... to set the temporary directory for Bioformats Memoizer. Use any temporary directory available on your system. The created files can be removed any moment.

BM3D installation directory: a text field and ... to set the path to BM3D 4.0 or newer (MATLAB version only), see more in the System requirements section.

Directory to store network architectures for DeepMIB: a text field and ... to set the DeepMIB and SAM network storage paths.

Fiji installation directory: a text field and ... to set the path to Fiji, see more in the System requirements section.

Imaris installation directory: a text field and ... to set the path to Imaris, see more in the System requirements section.

Java path (R2026b or newer): the Java that MIB uses for Bio-Formats, Fiji, Imaris and OMERO; MATLAB R2026b and newer come without Java. Find Java... lists the Java installations found on the computer, Configure Java... connects MATLAB to the selected Java, which takes effect after restarting MATLAB and MIB. A path changed without pressing Configure Java... is connected when pressing OK or Apply. See Enable Java for step-by-step instructions.

OMERO installation directory: a text field and ... to set the path to OMERO, see more in the System requirements section.

Python installation path: a text field and ... button to set the path to Python, required for SAM, see more in the System requirements section.

Python execution mode: a dropdown to choose how MIB launches the Python interpreter (used by SAM and other Python-based tools):

• OutOfProcess: Python and PyTorch run in a separate process with their own GPU (CUDA) context (default, recommended).
• InProcess: Python runs inside the MATLAB process, sharing its GPU context.

Keyboard Shortcuts¶

Customize key bindings for quick access to MIB actions:

• Shortcuts Table: A table to edit key bindings. Click a cell to assign a key combination.
• Pressed Key: A label showing the last key pressed (e.g., Ctrl + S) when the panel is active. Click the panel and press a key to test.
• Reset: A button to restore default key shortcuts.

Segmentation Tools¶

Adjust settings for segmentation tools, including interpolation, annotations, and favorites.

Annotations¶

Customize how annotations appear:

Font size:: a dropdown for annotation font size: - Options: 1 (pt 8), 2 (pt 10), 3 (pt 12), 4 (pt 14), 5 (pt 16), 6 (pt 18), 7 (pt 20) (default: 1).

Extra depth to show:: a spinner (minimum 0) to extend annotation visibility across slices (e.g., 3 shows annotations 3 slices before and after).

Color: a button to pick the annotation color (same as in Colors and Styles).

Interpolation¶

Configure how MIB interpolates between points:

Type: a dropdown to choose the interpolant:

• shape: Best for blobs (default).
• line: Suited for non-closed linear objects.

Number of points: a numeric field for points used in interpolation. Higher values improve quality but slow performance.

Line width, px: a numeric field for the thickness of lines in line interpolation.

Favorite Tools¶

Set quick-access segmentation tools:

Favorite tool A: a dropdown to select a tool accessed via Shift+D:

• Options: 3D ball, 3D lines, Annotations, Brush, BW Thresholding, Drag & Drop materials, Lasso, MagicWand-RegionGrowing, Membrane ClickTracker, Object Picker, Segment-anything model, Spot (default: Brush).
  
  
• Favorite tool B: a dropdown to select a tool accessed via Ctrl+D:
• Same options as Favorite tool A (default: Segment-anything model).

Input / Output¶

This category configures reading and writing of OME-Zarr v3 (.zarr3) datasets, used by the BigData and virtual dataset modes.

Zarr library¶

Zarr library: a dropdown to select the engine used for reading and writing zarr data:

• native: the bundled zarrMex engine - no external dependencies (default, recommended).

• python: the zarr-python library, called through the Python interpreter set in External directories → Python installation path. Requires the zarr and numpy packages installed in that environment. Reading a remote (HTTP/HTTPS) store with this engine additionally requires aiohttp and requests, which zarr-python uses to fetch chunks over the network:

  "<path-to-python.exe>" -m pip install aiohttp requests
  

A short description of the selected library is shown in the label beneath the dropdown. The setting takes effect immediately on OK / Apply - no restart needed.

Chunk Cache: memory, in megabytes, held for decoded zarr chunks (default: 512). Applies to zarr v2 and v3, local and remote, both engines.

A chunk is the smallest unit a zarr store hands over, and volumes are commonly chunked for 3D access rather than for browsing one plane at a time - 64 x 128 x 128 is typical, meaning every chunk carries 64 slices. Without a cache each slice change re-fetches and re-decodes those chunks and keeps only one plane of each. With it, the other 63 slices are already in memory.

The effect is dramatic on a remote store and still worthwhile locally, where it saves the decode rather than the download. Measured on a remote OME-Zarr v2 volume at full resolution: ~2 s per slice change without the cache, ~0.01 s with it, and panning back to a region already visited is equally free.

Set it to 0 to disable caching entirely - the escape hatch on a machine short of memory. When the budget is reached the least recently used chunks are dropped, so the figure is a ceiling, not an allocation. Lowering it releases the memory as soon as Apply is pressed.

The same value can also be changed in the Import from URL / Zarr dialog, where it takes effect without pressing Apply.

Smoothing: a checkbox controlling how a segmentation edit made at a low-magnification (zoomed-out) level of a BigData model is propagated into the higher-resolution pyramid levels (default: enabled).

• When enabled, coarse edits are reconstructed with a signed-distance transform so boundaries appear as smooth curves instead of blocky steps when you zoom in.
• When disabled, a faster nearest-neighbour upsampling is used, leaving blockier boundaries.

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