WoundHealing¶

class controllers.WoundHealing¶

Bases: handle

WOUNDHEALING - Controller for the Wound Healing Assay and Stitching dialog.

Provides grid stitching of zero-overlap image collections and wound healing assay analysis using the cellMigration algorithm (Reyes-Aldasoro et al., Electronics Letters, 2008).

Note

The wound healing analysis requires cellMigration.m to be on the MATLAB path. It is available in the MIB2 distribution under Tools/CellMigration/.

Launch as GUI tool:

obj.mibController.startController('controllers.WoundHealing');

Launch in batch mode (runs Stitch):

BatchOpt.Extension = 'tif';
BatchOpt.NoRows    = {3, [1 Inf], 'on'};
BatchOpt.NoColumns = {3, [1 Inf], 'on'};
BatchOpt.SelectedDirectories = {'C:\dir1', 'C:\dir2', ...};
obj.mibController.startController('controllers.WoundHealing', [], BatchOpt);

Trigger return of possible options:

obj.mibController.startController('controllers.WoundHealing', [], NaN);

Constructor Summary

WoundHealing(mibModel, varargin)¶

WOUNDHEALING - Constructor.

Syntax:

obj = WoundHealing(mibModel)
obj = WoundHealing(mibModel, [], BatchOpt)
obj = WoundHealing(mibModel, [], NaN)

Property Summary

BatchOpt¶

cell array of listener handles

listener¶

handle to main MIB figure (used as parent for dialogs)

mibGUI¶

handle to the view (views.WoundHealingGUI)

mibModel¶

view¶

handle to MibModel

Method Summary

static ViewListner_Callback2(~, evnt)¶

VIEWLISTNER_CALLBACK2 - Static listener guard; safe even when view is invalid.

addCallbacks()¶

ADDCALLBACKS - Wire all widget callbacks after view creation.

closeWindow()¶

CLOSEWINDOW - Destroy view and fire CloseEvent.

helpButton_Callback()¶

HELPBUTTON_CALLBACK - Open plugin documentation in browser.

returnBatchOpt(BatchOptOut)¶

RETURNBATCHOPT - Send BatchOpt to mibBatchController via SyncBatch event.

selectDirectoriesButton_Callback()¶

SELECTDIRECTORIESBUTTON_CALLBACK - Select input directories via multi-select dialog.

Uses uigetfile_n_dir to pick one or more directories in a single Java-based dialog. The selection replaces the current list.

selectOutputDirectoryButton_Callback()¶

SELECTOUTPUTDIRECTORYBUTTON_CALLBACK - Choose output directory via dialog.

stitchButton_Callback()¶

STITCHBUTTON_CALLBACK - Stitch a grid of images from selected directories.

Each selected directory must contain images corresponding to one tile position. Directories are ordered left-to-right, top-to-bottom. All directories must contain the same number of files (time points).

Saves stitched images and a time-stamp log to OutputDirectory.

updateBatchOptFromGUI(event)¶

UPDATEBATCHOPTFROMGUI - Sync BatchOpt from a widget change event.

updateOutputPath(value)¶

UPDATEOUTPUTPATH - Validate and store output directory from the edit field.

updateWidgets()¶

UPDATEWIDGETS - Refresh widgets to reflect current model state.

woundHealingButton_Callback()¶

WOUNDHEALINGBUTTON_CALLBACK - Run wound healing assay on selected directories.

Detects the wound width in each image using cellMigration and exports results as .mat and .xlsx files. Annotated images are saved under a snapshots/ subfolder of each input directory.

Requires cellMigration.m on the MATLAB path. Reference: C.C. Reyes-Aldasoro et al., Electronics Letters, 44(13), 2008.