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(4 edits)

Hi! Thanks for the suggestions, and nice work! I'll keep it in reference if opportunities arise. 
It's past morning and i need to get working on other projects, so please pardon some brevity on some of the points, but here goes:

(1) i'll investigate this if i come across an opportunity. With more important features on my roadmap this goes pretty low priority wise, but it may happen.

(2) is already in, though there's no menu item for it. Hit the [pause] key to make the editor semi-transparent. Then, i scale what i want to trace behind in a picture viewer or browser and place one of the canvases abovoe it. 

(3) Something like this is planned for. Though, may i suggest not trying to fit the full range of character animations in the same session? Even if the tool allows for up to 256 metasprite animation frames in a session, it's not recommended. It becomes a lot easier to manage if breaking it down to one or a few moves per session. 
Once animation features are in, it will be *a little* easier to manage large collections in a single session, but i will probably still recommend to break it up. 

(4) A scanline event emulator is planned for, but a bit down the priority list.

5) This is the artists' job, not the programs - It requires artistic consideration and intent to make such decisions, IMO.

6) i feel like this issue can be circumvened if you treat the logo as one asset for one session file, and the menu choices as one asset for another.  It's sort of the job of the NES program to put them together on-screen, and would bring better results than trying to mash it all into 256 tiles. If fitting it into 256 tiles (a reasonable target budget) still, it's better to design/draw/scale it with artistic means than trying to lossy-compress it. Lossy compression would just increase the amount of work that needs to be done to repair it, IMO.

(7) is already in. Use the bitmask toggles in the CHR Editor to draw/bucket/rotate/flip and most of all paste the 2 bitplanes individually. This way, you can merge and split graphics for use as 2bpp or "faux" 1bpp.  

When i convert 2bpp assets to layered 1bpp assets, i usually have at least 2 instances of NEXXT up. One for the source, then paste it to the desired bitplane of the destination instance. 
Note that most CHR Editor tools work on a selection bigger than what is viewed in its tile canvas. You can paste a full sets' worth of 1bpp data if you want to.