![HD TMA 2 2011 H&E stain.svs-[1499,1169,42287,37957]1x.png](/episphere/tma-grid/blob/main/HD%20TMA%202%202011%20H%26E%20stain.svs-%5B1499%2C1169%2C42287%2C37957%5D1x.png){kind=link}
TMA-Grid is a free, open-source, zero-footprint web application for tissue microarray (TMA) de-arraying. It segments cores in a whole-slide image, builds the virtual grid, lets you edit core metadata, and exports individual cores, all in the browser. No image is uploaded to a server.
Live app: https://episphere.github.io/tma-grid/
Manuscript: Ge A, Saha M, Duggan MA, et al. TMA-Grid: an open-source, zero-footprint web application for FAIR tissue microarray de-arraying. BMC Bioinformatics. 2026. https://link.springer.com/article/10.1186/s12859-026-06638-2
Video tutorial: https://youtu.be/miajqyw4BVk
- Upload a whole-slide image (
.svs,.tif/.tiff, or.ndpirecommended;.pngand.jpgwork with limited virtual gridding), load the demo image, open an image URL, or connect Box. - Segment the cores. Tune the preset, mask alpha, sensitivity, and core area limits, then add or remove cores by clicking the image.
- Grid the cores. Adjust the core radius and image rotation, drag cores into place, double-click a core to edit its metadata, and use the review queue to work through flagged cores.
- Export from the virtual grid. Double-click a core to export it at full resolution (
.svsonly), export the whole grid, and download the metadata as JSON or CSV.
The app is static HTML, CSS, and JavaScript. Serve the repository root with any static file server, for example:
python3 -m http.server 8000Then open http://localhost:8000/ in a browser.
If you use TMA-Grid in your work, please cite the manuscript:
Ge A, Saha M, Duggan MA, et al. TMA-Grid: an open-source, zero-footprint web application for FAIR tissue microarray de-arraying. BMC Bioinformatics. 2026. doi:10.1186/s12859-026-06638-2
Report bugs and request features at https://github.com/episphere/tma-grid/issues
See LICENSE.