Ruvan / dapi-counter

How to use

Upload a DAPI image of one or more organoids (JPEG, PNG, TIFF or HEIC). The tool finds each nucleus, outlines each organoid, and counts the nuclei that sit on its perimeter: those centred within the perimeter depth of the outline. Hover over an organoid to see its outline.

• Click a nucleus to switch it between perimeter and interior.
• Click an empty spot to add a nucleus the tool missed.
• Right-click (or shift-click) a nucleus to remove it. ⌘Z undoes.
• Hold the right mouse button away from any nucleus to see the image without markings.
• Numbers count each organoid’s perimeter nuclei clockwise from the top, then its interior ones, so the last pink number is the perimeter count. Press N to hide or show them.
• Click a row in the organoid table to leave that organoid out.
• Click “new group” (or press G), then click nuclei to count them as a group of their own. Each gets a yellow ring and a yellow number in the order you click. Click or right-click a nucleus again to take it out. Press Esc or click “new group” again to stop; turning it back on adds to the same group. Each image has one group, and it doesn’t change the organoid counts.

If counts look off across the whole image, adjust the sliders under Tuning; hand edits are kept when you do. Everything runs in your browser; images are never uploaded.