applyGIST2section_BATCHattempts to catch these occurrences, kill processes associated with a stalled section and restart them. The function works on Linux only (maybe on the Mac too if you can compile the DMG binaries for it). As of this writing, this approach works well but isn’t perfect. Please check, therefore, whether all sections have been produced before conducting further analyses. You can re-run
applyGIST2section_BATCHwith the overwrite flag disabled in order to generate any images that were missed the first time.
stitchedImages_100directory). In this directory are the stitched images and also a sub-directory called
detailsthat contains a CSV file for each stitched image. These CSV files log where the tiles are placed. The format is: top left pixel x position, width of tile in x, top left pixel y position, width of tile in y. The function
applyGIST2sectionuses this CSV file to construct a mask image. It applies this mask to the assembled section, produces the result, and returns the corrected image. The process is automated over a whole experiment with the
applyGIST2section_BATCH. Since the seam removal process requires only a TIFF image and a CSV file, it is possible write a wrapper in any programming language of your choice.