Disclaimer: I am not sure whether this is an error on my end or something to do with the software, so I’m putting this here in the Help section.
I’ve been using CP and Analyst for some time now while working with conventional, 3 channel microscopy images. Recently, I moved to a new project where we are using an MDS IXM to automate the process of acquiring z-stacks of cells printed in ~60 nL alginate blobs. The native files output by the device are stk, and so I’ve been trying to use Load Images with the stk option. Everything seems to work swimmingly except for one hang-up … only half of the slices from each stk seem to be loading and processing.
e.g. when I attempted to load a 60 slice stk of the blue (DAPI, in this case) channel and count nuclei, both the progress bar and the associated exported data file indicate that only 30 images are being processed. I repeated this again with a second set of stk’s I had acquired that had 100 slices in each, and this time it reads 50.
I’ve attached the pipeline (which is very basic … was just intended to test out working with the stk data type). The stk files are quite large (100+ MB), but if it is necessary to help figure out the problem, I can probably provide them via Dropbox sharing or something like that.
Any help / info / advice you may be able to provide would be greatly appreciated. Thanks!
stkPipeline.cp (4.51 KB)