Re: split image

Posted by ALR on Apr 20, 2015; 5:28pm
URL: http://imagej.273.s1.nabble.com/split-image-tp5001409p5012538.html

Dear Curtis, I am taking 4x4 confocal tiles with a 40x/1.4NA objective with 2x oversampling (following nyquist criterion); meaning, my slices are rather thin. Because of mounting and/or uneven illumination, the images in the tile are not in the same focal plane. To solve this, I have borrowed your code to split the titles into 16 images (thank you very much for the code, by the way), I then find the bottom of the cells in each image and crop stacks to the same dimensions for reassembly with all images in the same focal plane. Now I want to put the tile back together. In my splitting I named each image with coordinates _x{x}_y{y} so I could reassemble them using Preibisch's Grid/Collection Stitching Plugin. The problem is my slices are rather thin (0.33um) and after reassembling the image I obtain jumbled channels. I do not want to copy each slice several times to do the stitching (as recommended), just to have to remove them later. Each original tile is a bit shy of 1Gb as it is. If at all possible, I would rather put the tile back together the same way I took it apart. I have been trying to find a solution but it has evaded me. These images have no overlap, but I know how to put them together using the _x{x}_y{y} coordinates, is there a way to reassemble the 4x4 tile without FFT and data jumbling? What would you suggest? Thank you very much in advance!! All best, Andrés