I am working with Version 2.0, 32-bit. I’m transitioning from Version 1.0 because my computer just can’t handle it any more. I don’t know why, probably because of new Windows updates. I’m working with Windows XP Professional, Service Pack 3. I know it’s old, but I can’t afford to replace it.
Now, I am having a lot of problems with this new version.
For example, I’m having a number of stability problems with one of my pipelines. Sometimes it works, but on the next run, it crashes.
This is the PIPELINE:2_CropStack_IndividualCellsPIPE.mat (12 KB)
The goal of the pipeline:
I am trying to pick out individual cells of an image. I am cropping individual red-staining target cells from a red master image, and using that cropped image to identify and crop identical regions of subseqent planes of the stack (green images, not that it matters). You have to trace a single cell on the IdentifyObjectsManually module, Crop out just that region, Align the cropped individual cell to the same region on each of the subsequent green images, Crop each of those and Save each. The goal is to identify and crop cells corresponding to multiple red cells within the same field, one at a time. The PIPELINE works great the first time, and maybe even the second consecutive time. But if i try to use it multiple times one after another, it crashes at one of a number of steps. This might not be the most efficient way to do it. I had an alternative PIPELINE in Version 1.0, but it doesn’t work in 2.0 because of a bug in the Save Outline step.
It most often crashes in one of the CROP modules with the following error message:
Traceback (most recent call last):
File “cellprofiler\pipeline.pyc”, line 309, in run
File “cellprofiler\modules\crop.pyc”, line 339, in run
IndexError: index (1023) out of range (0<=index<1022) in dimension 0
It sometimes fails to identify the cell that I traced in IdentifyObjectsManually when it gets to the first CROP module. It sometimes crashes in the Align step. Usually it gets through these steps successfully, and crashes on the second CROP module. Unfortunately these aren’t happening today, so I can’t get you an error message.
Why would the pipeline work sometimes, but not others? It usually fails on the second or third consecutive run. Is something happening to the code, or could it be having a difficult time clearing its memory between runs? The PIPELINE needs to use the same set of starter images, but to identify and crop out different cells on each subsequent run.
Do you have any insight?
Thank you very much.