Choosing a file format for scientific images can be tricky. It seems simple enough on the outside, but the details turn out to be full of nuance and gotchas. Plenty of papers and presentations are spoiled by low quality images. Don't let yours be one! Get to know your image editor (I recommend GIMP), and your formats.

What determines quality?

The factors determining the quality of an image are:

• The number of pixels in the image (aim for 1 million)
• The size of the image (large images need more pixels)
• If the image is compressed, e.g. a JPG, the fidelity of the compression (use 90% or more)
• If the image is indexed, e.g. a GIF, the number of colours available (the bit-depth)

Beware: what really matters is the lowest-quality version of the image file over its entire history. In other words, it doesn't matter if you have a 1200 × 800 TIF today, if this same file was previously saved as a 600 × 400 GIF with 16 colours. You will never get the lost pixels or bit-depth back, though you can try to mitigate the quality loss with filters and careful editing. This seems obvious, but I have seen it catch people out.

JPG is only for photographs

Click on the image to see some artifacts.The problem with JPG is that the lossy compression can bite you, even if you're careful. What is lossy compression? The JPEG algorithm makes files much smaller by throwing some of the data away. It 'decides' which data to discard based on the smoothness of the image in the wavenumber domain, in which the algorithm looks for a property called sparseness. Once discarded, the data cannot be recovered. In discontinuous data — images with lots of variance or hard edges — you might see artifacts (e.g. see How to cheat at spot the difference). Bottom line: only use JPG for photographs with lots of pixels.

Formats in a nutshell

Rather than list advantages and disadvantages exhaustively, I've tried to summarize everything you need to know in the table below. There are lots of other formats, but you can do almost anything with the ones I've listed... except BMP, which you should just avoid completely. A couple of footnotes: PGM is strictly for geeks only; GIF is alone in supporting animation (animations are easy to make in GIMP). 

All this advice could have been much shorter: use PNG for everything. Unless file size is your main concern, or you need special features like animation or georeferencing, you really can't go wrong.

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