Wound healing scratch assay analysis.

Cytomove is a local-first browser workspace for wound healing scratch assay images: single images, groups, masks, plots, and exports. Your microscopy images stay on your device.

Open Web App Download Desktop App Guided tutorial
Images stay local Area and width metrics CSV, Excel, PNG, ZIP bioRxiv preprint

Everything needed for a practical web review.

The web app is the default entry point. It is meant for quick local analysis, figure checks, grouped time courses, and export without installing anything.

Local image input

Drag and drop one image or multiple time-point images. PNG, JPEG, BMP, GIF, and WebP are browser-friendly.

Segmentation controls

Brightfield and phase presets, threshold level, variance radius, component filtering, FOV crop, and rotation tools.

Area and width metrics

Wound area percentage, mean and median width, width spread, valid rows, area-width fit, and closure summaries.

Group plots

Review grouped images, preview time-course cards, open area and width plots, and export plot ZIP files.

Manual correction

Add scan, fill area, erase scan, clean specks, undo edits, and reset correction when the automatic mask needs review.

QC guidance

Segmentation quality score, warnings, component counts, continuity checks, and recommended primary metric.

Export formats

Download PNG overlays, group PNG ZIPs, plot ZIPs, CSV data, and Excel-compatible tables.

Privacy posture

Open images normally, then analyze them in the browser. The current web workflow keeps assay image files on your device.

Three simple steps.

Open the web app, load images, review the output, then export the pieces you need.

01

Load images

Use the toolbar or drag and drop. One file opens single mode; multiple files create a group.

02

Review and correct

Check contours or masks, adjust segmentation, crop, rotate, and apply manual correction if needed.

03

Export results

Save overlays, plots, CSV, or Excel tables for reporting and validation notes.

bioRxiv preprint validation

Compared with ImageJ/Fiji WHST, with every mask visible.

Cytomove was evaluated against ImageJ/Fiji Wound Healing Size Tool outputs across 31 paired measurements from five image sets. In the clean brightfield comparator sequence, Cytomove closely reproduced WHST wound-area trends (Pearson r = 0.9975), while keeping each segmentation visible as an overlay before export.

r = 0.9975 Clean brightfield comparator sequence versus WHST
31 Paired Cytomove-WHST measurements
5 Image sets spanning brightfield, phase contrast, and phone acquisition
Read the bioRxiv preprint View validation data Open Cytomove

Thank you for using Cytomove. I hope it is useful in your work. Please remember to cite the bioRxiv preprint when you use it in your analysis, figures, or methods. Duzgun, Z. (2026). Cytomove: a browser-local and reviewable workflow for scratch wound healing assay quantification. bioRxiv. https://doi.org/10.64898/2026.06.06.730617

WHST versus Cytomove wound-area agreement plots
WHST versus Cytomove wound-area agreement across the preliminary validation sets.
Area and width time-course agreement cropped from Figure 6 panels A and B
Independent time-course agreement, cropped to Figure 6 panels A and B.

Get the desktop app.

The web app stays the main public path. The Windows desktop app adds faster local group workflows and heavier ZIP exports, and is available to verified academic access accounts - just sign in to download.

  • Free for academic use.
  • Sign in with email or Google to unlock the installer and portable download.
  • Installer for everyday use, or a single portable .exe to run without installing.
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