This is a brief rundown of the steps necessary for opening the extracted sprites in photoshop.
I'll put together a tutorial on putting them back in later tonight possibly.
(Here is a little kit including a swatch library of possible NES colors and some helpful actions)
Fire up your terminal and run the tool on your ROM:
./NESRomTool <filename> -xs <chrIndex> <spritIndex> <toFile>
It will extract from the ROM
<filename> and put it into
<toFile> should have the .raw extension)
Fire up Photoshop and select the .raw file you extracted.
Set your settings as shown...
Set the color mode to "Indexed Color"
Select "Color Table..." from the Mode submenu to bring up the color table window...
Set the first 4 colors to whatever you want (the rest of the colors are unused).
You can click and drag over the first 4 boxes, then pick a start and end color. Photoshop will interpolate the colors in between.
There you have it, a sprite! Have fun editing!
When you're done, you just save the file as raw again from Photoshop and you can inject it back into the ROM like:
./NESRomTool <filename> -is <chrIndex> <spritIndex> <fromFile>