Hello,

I am trying to create a pipeline which stitches together four fields from a single channel per well taken on an InCell6000. My current method is fairly clunky which requires me to first copy and rename the images to a predictable format and put them in a plate directory with well subdirectories. I then copy this file over onto my computer where I run a separate ImageJ macro. I wrote this macro so that it prompts an input and output directory. It then loops through each well and stitches together the fields based off of a roughly estimated position (based off the file name), rastering pattern, percent overlap and image content. After which it writes the image out into the output directory (OutputDir>Well>Img.tif). This method is fairly tedious, but does a very good job at stitching the images together making it bearable. For these reasons I would like to integrate the entire method into single pipeline, which I am sure can be done.  To do so I need to be able to write the files into a user directory and run the ImageJ macro without having to open input images. To make this more challenging the run ImageJ on server and on client components crash when attempting to run the macro, but work fine for all other purposes? So it is not a problem with ImageJ itself. Has anyone had experience with a problem such as this?

-Reid