What is your recommendation about integrating “Multispectral Imaging” (the previous name of the MicaToolbox directory in ImageJ) with “micaToolbox” (the new name of the directory included in the download of 2.0)? Is there any problem with adding the contents of “micaToolbox” (from the download of 2.0) into the existing “Multispectral Imaging” directory, or is the recommendation to essentially ‘start-fresh’ by using “micaToolbox” and adapting any custom scripts/macros to the new toolbox? Thanks for the great work and toolkit!
You should definitely create a fresh installation of ImageJ for using with the new version of the toolbox. i.e. download and unzip the latest versions of ImageJ and the micaToolbox to a different location on your computer.
However, mspec images made with previous versions of the toolbox are compatible with version 2 of the toolbox. The main difference is that when images are opened they are on a percentage reflectance scale (e.g. 0-100%), and cone-catch values are on a 0-1 scale (though numbers can and do go above these maximum values). In the previous version the images were all on a 16-bit scale, which was unnecessarily confusing!