create or modify your sprite directly on Godot engine github : https://github.com/SoloCodeNet/godot-sprite-editor-addon
copy the folder addons/pixel_ever/ into your project
and enable your plugin in the Project settings / plugins
now when you select a sprite node, a tab named "Sprite Editor" is available on bottom (you can expand it ahead)
you have 4 tools:
- Draw with pen left click for color / right click to erase
- Pick Color for select a specific color on sprite
- Replace Color for replace alls old color with the new selected color
- paint Bucket for fill with the new color
you can change the palette on bottom with 4 differents palettes available. you can add new palettes on folder addons/pixel_ever/pal/ and use it directly (respect the 128pixel size format)
the save button modify the sprite if exist or ask you where and who to save the new sprite