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MIB Plugin without GUI

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Overview

Plugin without GUI

The MIB Plugin Without GUI is a tutorial example for creating plugins for Microscopy Image Browser (MIB) without a graphical interface.
It demonstrates how to build a simple plugin that prompts the user for a threshold value and generates a mask layer by thresholding the current image slice.

This plugin serves as a starting point for developers to understand MIB plugin architecture and customize functionality for their needs.

Understanding of sections

Filenames

The plugin without GUI has only a single file that is called as [PLUGIN-NAME]Controller.m, where [PLUGIN-NAME] is the name of the plugin.

Warning

This name should match with the name of the directory where the plugin is located.

Example

For example mibPluginWithoutGUIController.m:

  • [PLUGIN-NAME] -> mibPluginWithoutGUI, located under Plugins/Tutorials/mibPluginWithoutGUI directory
  • Full path: MIB/Plugins/Tutorials/mibPluginWithoutGUI/mibPluginWithoutGUIController.m
Plugins with GUI

Plugins with GUI will also have additional files.

  • GUIDE based plugins have [PLUGIN-NAME]GUI.m and [PLUGIN-NAME]GUI.fig files that are created by MATLAB guide editor. (e.g. MyPluginGUI.m and MyPluginGUI.fig. These, together with MyPluginController.m should be placed under MyPlugin directory). See more here
  • AppDesigner based plugins have [PLUGIN-NAME]GUI.mlapp created by MATLAB appdesigner editor. (e.g. MyPluginGUI.mlapp. This file, together with MyPluginController.m should be placed under MyPlugin directory). See more here.

properties

This section can be used to define properties of the plugin class. These properties will be available to all functions withing the plugin class

properties
    mibModel
    % handles to the model
    noGui = 1
    % a variable indicating a plugin without GUI
end

events

This plugin has a single event that is triggered when the plugin is closed. 

events
    %> Description of events
    closeEvent
    % event firing when plugin is closed
end

constructor

Constructor is the first function that is initialized when the plugin starts.

mibModel that holds data classes of MIB is passed as a parameter and assigned into obj.mibModel variable available to all functions of the plugin.

The following section checks whether MIB is in the virtual stack mode and closes the plugin in this case without any output

obj.calculateBtn_Callback() command starts the main function of the plugin

function obj = mibPluginWithoutGUIController(mibModel)
    obj.mibModel = mibModel;    % assign model

    % check for the virtual stacking mode and close the controller
    if isprop(obj.mibModel.I{obj.mibModel.Id}, 'Virtual') && obj.mibModel.I{obj.mibModel.Id}.Virtual.virtual == 1
        warndlg(sprintf('!!! Warning !!!\n\nThis plugin is not compatible with the virtual stacking mode!\nPlease switch to the memory-resident mode and try again'), ...
            'Not implemented');
        return;
    end

    obj.calculateBtn_Callback();  % start the main function
end

Adapting the function to a new plugin

Perform the following operations to use this plugin as a template for a new plugin.

  • Create a folder for your plugins under MIB/Plugins/ for example MyPlugins so that the full path is
    MIB/Plugins/MyPlugins
  • Create a subfolder under MIB/Plugins/MyPlugins and name it with the name of your new plugin (e.g.MIB/Plugins/MyPlugins/MyFirstPlugin)
  • Copy mibPluginWithoutGUIController.m to MIB/Plugins/MyPlugins/MyFirstPlugin
  • Rename mibPluginWithoutGUIController.m to MyFirstPluginController.m
  • Open MyFirstPluginController.m in MATLAB
  • Do Find and Replace to search for mibPluginWithoutGUI and replace with MyFirstPlugin, Ctrl+F key shortcut.
Snapshot

Granularity plugin

  • Edit calculateBtn_Callbackto implement your desired functionality, such as:

    • Processing multiple slices.
    • Applying different filters (e.g., edge detection).
    • Exporting results to a file.

  • Save the plugin

  • Restart MIB to refresh the list of plugins.
  • Run your plugin from Menu → Plugins → MyPlugins → MyFirstPlugin.

Calculate function

This is the main function of the plugin, upon completion, the plugin is closed. Everything within this function can be replaced with a custom code.

function calculateBtn_Callback(obj)
    % start main calculation of the plugin

    % ----- below a small test, replace it with your own code

    global mibPath; % get global mibPath variable 

    % setup question dialog to get thresholding value
    prompts = {'Threshold value:'}; % question prompt
    defAns = {'128'}; % default answer
    dlgTitle = 'Threshold image'; % dialog title
    % additional explamation text
    options.Title = sprintf('You are going to test mibPluginWithoutGUI plugin of MIB\nThe plugin will threshold the current slice using the provided threshold value and assign it to the Mask layer');
    options.TitleLines = 3; 
    % generate the dialog
    answer = mibInputMultiDlg({mibPath}, prompts, defAns, dlgTitle, options);
    if isempty(answer); return; end 
    % convert the provided answer from string to double
    threhsoldValue = str2double(answer{1});

    wb = waitbar(0, 'Please wait'); % add a waitbar to follow the progress

    [height, width, ~, depth] = obj.mibModel.I{obj.mibModel.Id}.getDatasetDimensions('image');  % get dataset dimensions
    img = cell2mat(obj.mibModel.getData2D('image'));    % get the currently displayed image
    waitbar(0.5, wb);   % update the waitbar

    mask = zeros([height, width, depth], 'uint8'); % allocate space for the mask layer
    mask(img<threhsoldValue) = 1; % threshold image
    waitbar(0.95, wb);     % update the waitbar

    obj.mibModel.setData2D('mask', mask); % send the mask layer back to MIB
    delete(wb);         % delete the waitbar

    % notify mibModel to switch on the Show mask checkbox, 
    % which also redraws the image
    % alternatively, 
    % notify(obj.mibModel, 'plotImage');
    % can be used to force image redraw
    notify(obj.mibModel, 'showMask'); 
 end

Credits

Author: Ilya Belevich, University of Helsinki (ilya.belevich@helsinki.fi)

Part of: Microscopy Image Browser (https://mib.helsinki.fi)

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