Tiles get scrambled at random when importing 2d images from czi. If czi has multiple channels, all the channels in the tile are scrambled. Following code used to import czi and write nrrd files for each channel. https://github.com/gbkedar/farsight/blob/IlluminationGraphCuts/IlluminationCorrection/readCziWriteCorrectedTiles.cpp Sample images sent to Mark Hiner.