Failed Tiling Images due to non conventional tiling pattern

Hello! I’ve attached the first 4 files of an image set of 12 (b/c Im a new user I can only post 5 at once) I’m attempting to tile from the EVOS m7000. The software is silly bc it collects the images starting at the middle of the well, and in a “serpentine clockwise” position. When I try to tile using CellProfiler, I can only select starting from the corners. I keep getting mis-tiled images or black files exported. I’ve tried telling it the number of rows or columns, to help it along but nothing is working. There aren’t many options in this module, so I’m wondering if anyone has suggestions or if i"m better off with imagej. I just don’t konw how to batch process these files on image J, considering there are multiple timepoints, and channels in the same folder. Thanks in advance for any help you can offer.

21-01-29_Plate_R_p00_0_A01f00d4.TIF (5.4 MB) 21-01-29_Plate_R_p00_0_A01f01d4.TIF (4.9 MB) 21-01-29_Plate_R_p00_0_A01f02d4.TIF (5.2 MB) 21-01-29_Plate_R_p00_0_A01f03d4.TIF (5.0 MB) tiling.cpproj (831.8 KB)

You’re correct that I don’t think CellProfiler can support tiling in that fashion at present. It’s something we may consider adding in the future, but until we do, ImageJ’s Grid/Collection Stitching is my stitching/tiling software of choice.


The other option would be to make sure CellProfiler loads your images in an order that allows you to use its inbuilt stitching- basically, renaming them so -1 is the one you want in the first position, etc. It could certainly be done, but I’d just use ImageJ.