That seemed to work -- sometimes. But it's probably best to simply produce each graphic separately, then embed as a png in the org file.

On Wed, Feb 17, 2016 at 8:54 AM, Eric S Fraga <e.fraga@ucl.ac.uk> wrote:
On Tuesday, 16 Feb 2016 at 19:22, Lawrence Bottorff wrote:
> I've got this code:

[...]

> running in an org file, and it gives me embedded images in an html
> file. (See this). But they're cramped and have a strange gray
> background. How can I not clip and get the png transparent working?

I added these options to the src block

 :imagemagick yes :iminoptions -density 600 :imoutoptions -geometry 800

and the first src block works for me: images are proper size and the
background is transparent.  I could not test the second as I don't have
qtree.

The process might depend on what your system uses to generate the images
from LaTeX.
--
: Eric S Fraga (0xFFFCF67D), Emacs 25.0.91.1, Org release_8.3.3-601-gff9890