Pixel Cleanup - Pixelate Pro

Downscaled 3D often leaves lone pixels that don’t belong: a speck of a different shade, a one-pixel hole, a bump on an edge. They look noisy and flicker between frames. Pixel Cleanup removes them while keeping deliberate details such as 1 px lines and eyes.

A character with Pixel Cleanup off, Light and Strong, with the changed pixels highlighted

In the image, the “changes” columns highlight what was touched: magenta pixels were recolored or filled, cyan pixels became transparent.

Settings

Setting	What it does
Strength	Off changes nothing. Light (default) removes single pixels of a similar shade to their surroundings and fills single-pixel holes. Strong also removes higher-contrast single pixels and lone pixels floating outside the sprite, and smooths 1 px bumps and dents in the silhouette.
Remove Orphan Pixels	Recolors a single pixel that matches none of its neighbors when most of the pixels around it share one similar color. Pixels that continue a line are never changed. At Strong, it also removes lone pixels outside the sprite. Light keeps those, for example sparks in an effect.
Fill Pinholes	Fills a single transparent pixel that is surrounded by the sprite.
Smooth Silhouette	Strong only. Removes a 1 px bump on a straight edge and fills a 1 px dent. Line tips, 1 px gaps and diagonal steps are kept.

Use the three checkboxes to switch off a single rule while keeping the rest.

Good to know

Pixel Cleanup never adds new colors. Every changed pixel copies a neighbor or becomes transparent, so the result stays inside your palette.
It runs after Color Palette and Lighting and before Dithering, so it never erases dither patterns.