correctZilluminationInDirectory, which has the option of either replacing the original stitched data or placing the corrected sections in a new directory, allowing for comparison with the originals. Avoid retaining multiple versions of the same stitched stack with slightly different corrections in place. This is a recipe for creating terabytes of redundant data. Re-stitching is cheap, so maintain only the data you need. Bellow show the before and after effects of z-illumination correct.
rawData/stitchitPreProcessingFilescontains the average tile illumination data from each section as well as various other statistics. Grand average tile averages are stored in
rawData/averageDirand generated by
collateAverageImages. For example the file
rawData/averageDir/2/01_bruteAverageTrimmean.matcontains correct data for channel 2 optical plane 1. You can load this structure and look at it in MATLAB:
pooledRowsto remove the illumination artifacts. Which it uses is defined by the
splitcauses a different correction to be used for the odd and even rows.
poolcauses a single correction to be used for all tile rows.
poolshould suffice in most cases. If you notice odd issues with the illumination correction, first try setting
0and restitch (or use
peekSection) to see what your data look like. You can also
imagesc avData.pooledRowsto see what the average tile looks like. If there is some problem with the average tile, this will manifest in the stitched image. You could try using grand averages from a different experiment or from a different channel if weird stuff is happening.
applyGIST2section_BATCHcommands. The results are usually very effective: