Overview # There are four steps to this process. First is to create a dataset file that allows BigSticher to interpret the data. Second is to run a macro that will flip the opposing views, so they are roughly aligned. Third is to find the best parameters that register the views together. Forth is to register and export the reconstructed data. Inital Setup # First we must install ImageJ and the BigStitcher plugin. ...
For a recent blog post, I needed to get my hands on some Imaris IMS files. Fortunately for me, the good folks over at OME have a nice repository of example images in a variety of formats. The OME Team use this data for testing the read/write functions in their Bio-Formats library. I was particularly interested in downloading all of their Imaris images, but it appeared the only way to get the entire dataset was to manually download each file. I can’t waste that much time downloading files!
How to set up and use a MATLAB script to pull out ROIs in Lattice Light-sheet data.