Wound Healing Assay¶

Measures cell migration in scratch wound assays from time-lapse microscopy. Includes grid stitching for tiled image collections.

Overview¶

The Wound Healing Assay tool monitors cell migration into a scratch wound over time.

Demonstration

It operates in two independent steps:

Stitch — assemble a tiled (grid) image collection into a single stitched image per time point
Wound healing — detect wound width in each image and export results as plots, Excel, and MATLAB files

Launch via Ribbon → Tools → Wound Healing Assay.

Stitching settings panel¶

Assembles a grid of overlapping-free tile images (e.g. from Imagen Cell-IQ) into one image per time point.

No. Rows — number of tile rows in the grid (default: 3)
No. Columns — number of tile columns in the grid (default: 3)
convert to grayscale — average RGB channels to produce a single-channel stitched image
Extension: — filename extension for input images (default: tif)

Directory selection:

Select directories... — select input directories, one per tile, ordered left-to-right then top-to-bottom (i.e., row-major). The number of directories must equal No. Rows × No. Columns.
output directory / Output... — type or browse to the output directory where stitched images will be saved.

Stitch — starts stitching. Each time point is saved as <original-name>_stitched.<ext>. A text file with file modification timestamps is also written to the output directory.

Tip

When the extension is jpg, a quality prompt (0–100) appears before stitching begins.

Wound healing settings panel¶

Measures wound width at each time point using the cellMigration algorithm.

Pixel size — physical pixel size in µm (default: 1). Used to convert wound widths from pixels to µm.
Time step — time interval in hours between consecutive images (default: 1). Used to label the time axis in result plots.
Downsample resulting images — resizes annotated wound snapshot images to this percentage of their original size before saving (default: 50 %). Reduces disk usage for result snapshots.
show interactive plot — display a live plot of wound width (min / average / max) after each time point is processed.

Directory selection:

Select directories... — select one or more directories of stitched images to analyse. Each directory is processed independently.

Wound healing — runs the analysis. For each directory:

Detects wound boundaries per image using cellMigration.m
Plots minimum, average, and maximum wound width vs. time
Saves annotated images to a snapshots/ subfolder inside the input directory
Exports results to WoundAssayResults_<dirname>.mat and WoundAssayResults_<dirname>.xlsx

Warning

cellMigration.m must be on the MATLAB path. It is distributed with the MIB plugin under Plugins/WoundHealingAssay/.

Exported results¶

Output	Location	Content
`.mat` file	input directory	`results.minVec`, `results.maxVec`, `results.avVec` — wound width (µm) per time point
`.xlsx` file	input directory	Same data as a spreadsheet with image names, time points, and pixel/time step metadata
Snapshots	`snapshots/` inside input dir	Annotated wound images (`Wound_<original-name>`)
Timestamps	output directory	`<name>_TimeStamps.txt` — file modification dates for each stitched time point

Batch scripting¶

Batch mode runs the Stitch step only (wound healing requires interactive cellMigration output).

Example

BatchOpt.Extension           = 'tif';
BatchOpt.NoRows              = {3, [1 Inf], 'on'};
BatchOpt.NoColumns           = {3, [1 Inf], 'on'};
BatchOpt.SelectedDirectories = {'C:\data\pos1', 'C:\data\pos2', ...};
BatchOpt.OutputDirectory     = 'C:\data\stitched';
BatchOpt.ConvertToGrayscale  = true;

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

References¶

Based on Cell Migration in Scratch Wound Assays by Constantino Carlos Reyes-Aldasoro.

Cite as: CC Reyes-Aldasoro, D Biram, GM Tozer, C Kanthou, Electronics Letters 44(13), 791–793, 2008. Code available on GitHub.

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