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# Preferences

Back to MIB | User Interface | Menu | File

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 Menu -> File -> 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 six 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.

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).

Info

selecting any of these options swaps the mouse button so that takes the other role.

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

- `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.

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

Where to find recently used directories

the previously accessed directories available via a dedicated dropdown in the Path panel.

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.

### 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.

How to find scaling factor on Windows

Do on Windows Desktop and select Display settings
Find the scaling factor and type it as value in %% divided by 100 (i.e. `1` for the snapshot below):

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

Warning

The scaling is done relative to initial size of MIB widgets rendered at MIB startup

Checkboxes to choose which elements to scale

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.

Warning

Press of the button is always rescales MIB interface relative to the current state. If after the initial resizing step, you feel that additional scaling is needed, try to estimate how much the scaling factor needs to be relative to the initial size of MIB interface. Set this value and restart MIB!

## 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.

Manage color palettes for visualization via a context menu :

- 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.

Update material colors directly from the Segmentation table

The colors can be changed via a context ment of the Segmentation table -> Color scheme...

### 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

### 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.

### 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

Examples of different mask visualization styles

## 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.

Tip

The backup and undo system requires additional allocation of memory and slows down performance.
Balance memory usage and undo needs by setting reasonable history limits, especially for large datasets.

## External Directories

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

Fiji Installation Directory: a text field and ... to set the path to Fiji, see more in the System requirements section.
OMERO Installation Directory: a text field and ... to set the path to OMERO, 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.
BM3D Installation Directory: a text field and ... to set the path to BM3D, see more in the System requirements section.
M4D Installation Directory: a text field and ... to set the path to BM4D, see more in the System requirements section.
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.
Directory to Store Network Architectures for DeepMIB: a text field and ...to set the DeepMIB and SAM network storage paths.
Python Installation Path: a text field and ... button to set the path to Python, required for SAM, see more in the System requirements section.

## 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.

Warning

Ensure the Keyboard Shortcuts panel is selected to capture key presses for testing.

## 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).

Tip

Style for the annotations can also be specified in the Annotation list -> Settings window

### 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: 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).

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