Recognise this? Roundtripping chemical images

With the imminent release of Open Babel 2.3.1, I thought I'd come up with some examples of use for a new feature, PNG depiction.

To generate a PNG with Open Babel you just use the PNG output format:

obabel -:CC(=O)Cl -O tmp.png

Open Babel actually allows you to embed the chemical structure (in any format) directly into a new or existing PNG file. If you do this, then you can roundtrip as follows:

> obabel -:CC(=O)Cl -O tmp.png -xO smi
> obabel tmp.png -osmi
CC(=O)Cl

If you haven't embedded a chemical structure in the image, you'll have to use optical chemical recognition software such as the open source OSRA (Igor Filippov) or Imago (GGA Software). Both of these can output a MOL/SDF file, which contains the 2D coordinates of the perceived structure, and this can be depicted. I did this for a set of 450 images from the Japanese Patent Office as follows:

> for %a in (*.tif) do "C:\Program Files (x86)\osra\1.3.8\osra.bat" %a --format sdf | obabel -isdf -O %~na_osra.png -d
> for %a in (*_chem.png) do "C:\Program Files\GGA Software\Imago Toolkit\alter_ego.exe" %a -o tmp.mol -q && obabel tmp.mol -O %~na_imago.png -d

The results are here: Subset 1 2 3.

Notes:
1. Open Babel depiction for large molecules needs to be fixed, as the lines get faint and disappear in some cases. [Update (26/03/2012): Now fixed]
2. The tiff files needed to be converted to pngs for Imago (used a "for" loop with Imagemagick convert).
3. In the case of multiple molecules in the OSRA output, only the first molecule is depicted (I think).
4. Several structure gave error messages when depicting the Imago structures due to unrecognised labels. I think there's a way around this but I didn't look into it.