Microscopy Image Browser Preferences

This dialog provides access to preferences of Microscopy Image Browser. Allows to modify colors of the Selection, Model and Mask layers, default behaviour of the mouse wheel and keys, settings of Undo...

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Preferences
User Interface Tweaks
Program Settings
Segmentation Settings
Colors

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Preferences

Please note, MIB stores its configuration parameters in a file that is automatically generated after closing of MIB

Locations where configuration files are stored

for Windows - C:\Users\Username\MATLAB\mib.mat or in the Windows TEMP directory (C:\Users\User-name\AppData\Local\Temp\). The TEMP directory can be found and accessed with Windows->Start button->%TEMP% command
for Linux - /home/username/Matlab or local TEMP directory
for MacOS - /Users/username/Matlab or local TEMP directory

User Interface Tweaks

Mouse Wheel - allows to choose between two possible actions done with the mouse wheel. When Zoom is selected, rotation of the mouse wheel will result in zoom in/out action; when scroll is selected rotation of the mouse wheel will result in change of the shown slices. Note! the mouse wheel may be used together with Shift button to scroll more than one slice at the time, see more in Image View Panel/Extra parameters for the slider

Left Mouse Button, allows to select action for press of the left mouse button. When pan is selected the press and hold of the left mouse button will result in moving of the shown image to left-right and up/down directions. When select is selected the left mouse button can be used for making selections. Note! The left and right mouse buttons are mirrored, i.e. if one action (pan or select) is selected for the left mouse button, the right mouse button implements the second available action.

Image Resize Method. Modifies a way how image is resized during on screen zoom in/zoom out action. Use 'nearest' to see unmodified pixels and 'bicubic' for smooth appearance. Note! the nearest option gives the fastest and bicubic the slowest performance. It is also possible to toggle the this from a dedicated button in the MIB toolbar.

Disable Selection. When Selection is disabled it is not possible to use the Selection layer for segmentation. In this situation memory requirements are lower.

Select Font - this button starts a standard font selection dialog
Font size edit box - modifies default font size for all text panels
Font size for dir contents - modifies the font size for the list of files in the Directory Contents panel.
Shortcuts - shortcuts for keys may be customized using the Define shortcuts for keys dialog that is started with this button. The list of default shortcuts is available from the Key & mouse shortcuts page.

A brief demonstration is available in the following video:
https://youtu.be/qrLyrP9f018

GUI Scaling - starts an input dialog that allows to tweak scaling of varipous user interface widgets. This may be required when working with MIB on MacOS or Linux. Operating system scaling factor - this number is needed when the text size is increased on the operating system (on Windows: Control Panel\All Control Panel Items\Display\Screen Resolution->Make text and other items larger or smaller)

Program Settings

Modification of Undo parameters

A brief demonstration is available in the following video:
https://youtu.be/PrY3Eo02gU8

Enable - enable/disable undo. When the memory is limited it may be recommended to set the Enable undo setting to the no state.
History Steps - maximal number of history steps to keep in memory. Note! requires restart of Microscopy Image Browser to apply this modification.
3D History - number of 3D datasets that can be stored. When memory is limited it is recommended to set this value to 0. Note! requires restart of Microscopy Image Browser to apply this modification.

External dirs, starts a dialog to specify installation directories for Fiji, Imaris, Omero and BMxD filters. Please refer to the System Requirements pages for details. If there is no need to use any of these programs, remove all text from the path edit box.

Segmentation Settings

Type of interpolation, defines type and parameters of the interpolation for the Selection layer to use (i - shortcut, or Menu->Selection->Interpolate).
A brief demonstration is available in the following videos:
- Shape interpolation: https://youtu.be/ZcJQb59YzUA?t=4m3s
- Line interpolation: https://youtu.be/ZcJQb59YzUA?t=2m22s
Number of points - number of points to use for the interpolation, more points give smoother results, white the less points is faster
Line width - defines width of the line after the interpolation
Font size for annotations - defines size of annotation text, the annotations may be accessed from the menu entry: Menu->Models->Annotations
A brief demonstration is available in the following video:
https://youtu.be/3lARjx9dPi0

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Colors

Modification of default colors of the Annotations, Selection, Mask, Model layers and defining color look-up table (LUT). The upper table shows the list of predefined colors for Materials of the Model layer. The lower table shows LUT for colors of the color channels to use with the LUT mode (View Settings Panel-[✓] LUT checkbox>)

A brief demonstration is available in the following video:
https://youtu.be/A5HHVd5bfJ0

Modification of the Model and LUT colors. The rows in tables represent color in Red:Green:Blue format in range from 0 to 255. The colors may be modified either by updating the numbers in the tables or by clicking on a color bar (fourth column) representing the defined color.
Modification of the Selection colors. Press the Selection button to start the color selection dialog.
Modification of the Mask colors. Press the Mask button to start the color selection dialog.

Some actions are available for the colors of materials. These actions are available via a popup menu called using the right mouse button click above the upper table.

Reverse colormap reverses the existing colormap
Insert color inserts a random color to the colormap at position after the one that was selected
Replace with random color replaces the selected color with a random one
Swap two colors swaps two colors between each other
Delete color(s) deletes the selected color from the colormap. Multiple colors could be selected using the Shift+mouse click combination
Import from MATLAB imports a colormap from the main MATLAB workspace
Export to MATLAB exports the colormap to the main MATLAB workspace
Load from a file loads a colormap from a file. The colormap should be saved using the matlab format and cmap variable
Save to a file saves the colormap to a file. The colormap is saved using the matlab format and cmap variable

Built-in color palettes

There are several built-in palettes for coloring materials of models are available. The palettes may be selected using the Palette and Number of colors comboboxes. The Default color palette was selected so that each color appears as a distinctive shade to color-blind users.

Description of palettes

The color palettes done with help of following sources: