I’ve just released QuPath, which is entirely new, open source software for bioimage analysis.
If you are interested, you can find out more and download QuPath at https://qupath.github.io
If you are a biologist working with microscopy images, you might be interested in the following introduction to image analysis:
The optimistic aim in creating this was to help demystify light microscopy data, by outlining from (more or less) first principles the main ideas, concepts and techniques encountered when working with digital images. While the main emphasis is on fluorescence microscopy data, much of the content is applicable to all kinds of images.
Various questions, practicals and puzzles are strewn throughout the text, for which the following additional data is needed:
The text was created while I worked at the Nikon Imaging Center at Heidelberg University, and many of the real example images included are thanks to my marvellous colleagues there.
I’ve put this online in the hope it might be useful to someone. If you happen to read it and have any comments, corrections or suggestions, please let me know!
If you wish to link to this, please use http://go.qub.ac.uk/imagej-intro – linking directly to the PDF may stop working when it is updated, and doesn’t include the practical data . Thanks!