Talk:Converting microarray images

Hi Sven, was just wondering why you are converting tiff to jpeg? Jpeg is going to introduce a lot of artifacting and I imagine this would have a very bad affect on your results. If your source is TIFF consider using the LZW compression with binary encoding to save space and then translate this directly into PNG with imagemagick. In this way the only loss will be the pixel colour rounding error introduced with the conversion from 16bpp to 8bpp. This is still a lot of error though.

Check this: wikipedia:png. It looks like the PNG format supports 48bit colour spaces, so you could keep the whole 16bits per pixel in the conversion to PNG and not have to discard any data. --Rob 12:48, 14 Sep 2006 (NZST)

The problem is that the microarray images are proprietary 16-bit TIFF images of two channels plus a whole lot of auxillary information. If I use imagemagick to examing the filetype it think there are two images and converts them both to two separate PNG's (which is not what I want). I am forced to use the software that does the scanning of these images to convert to a lossy format first before making cut down PNG's. To reduce the loss I want JPG's that are as big in filesize as possible, we start with 110Mb TIFF's and convert to 40Mb JPEG's.

$ identify AT45.tif AT45.tif[0] TIFF 3760x8112+0+0 PseudoClass 65536c 16-bit 116.4m 1.1u 0:02 AT45.tif[1] TIFF 3760x8112+0+0 PseudoClass 65536c 16-bit 116.4m 0.5u 0:01

( --Sven 14:52, 14 Sep 2006 (NZST)

If imagemagick understands then it's sweet. Just grab your 2 channels and assign them to R and G and leave B and A blank. That way you have a RGBA compatible colour space. Save this out as a PNG. I haven't played with imagemagick but if it can deal with channels then it can construct as many as are needed. --Rob 16:47, 14 Sep 2006 (NZST)