Problem with pauses in 2.1.0

Hi all. Our lab has recently discovered CellProfiler and we are really excited to be working toward better faster data quantification in our IHC datasets.

As an introduction to what our lab does, we focus on development and patterning of an endodermally-derived organ primordium. When using CellProfiler, we use “Identify Objects Manually” to identify the primordium and then we use the automated features of CellProfiler to count cells and measure intensity for nuclear markers within the primordium. It works well and we are saving many hours relative to performing hand counts on our cells.

We recently upgraded to 2.1.0 on one of our lab machines and we love the speed of multi-core processing, but we are having a problem with pausing during the analysis. In the past, we had our pipeline set up to analyze a single image with a “Pause CellProfiler” module at the end. This would let us quickly check over each image and make sure that our “Identify Primary Objects” step worked with little to no error. This step was essential because variability between sections, slides, mutants, and controls could sometimes confuse the cell counting algorithms and give us false positives or missed cells. It slowed down our analysis a bit, but it has worked really well and let us verify our data at each step along the way.

In the new version, the “Pause CellProfiler” module has been removed and instead, there is a pause button in the main CellProfiler window. We could press this button after every every cycle to verify our work, but there is one major issue. The “Identify Objects Manually” window is constantly being refreshed because the human element of drawing the circle around the primordium is the bottleneck in our analysis. As long as the “Identify Objects Manually” window is present, we can’t click outside of that window. We cannot pause, nor can we click or on other CellProfiler windows to check the results from our “Identify Primary Objects” steps. Because we can’t click outside of the “Identify Objects Manually” step, this continues until our data (sometimes 70+ images) has been analyzed. It really is amazingly fast, but it leaves us no way to check our work as we go.

It would be really nice if we could pause at the end of each pipeline again, but it may not be possible with how CellProfiler is coded to run on multiple cores. Barring that, it would be awesome to be able to click outside of the “Identify Objects Manually” window so that we could use that step as a pseudo-pause and check our analysis. Are there any other workarounds for this? For the time being, we are still using the old version, but we would love to make the switch and perform our analysis on multiple cores.


Thanks for giving CellProfiler a try! The reason that the PauseCellProfiler module has been removed is that CellProfiler has a Test mode which is a much richer way of previewing your module results.

You can click the “Start Test Mode” button at the lower-left once your module are in place. You’ll see a new set of icons appear to the left of the module names, one of which is a pause button indicated by two vertical bars. Press the icon to put a pause in place at any point in the pipeline; then, if you press the “Run” button, the modules will execute until the pause is reached.

Also, you can select the image set of examine by selecting Test > Choose Image Set from the menu bar. This will allow you select which image to preview and then run/pause for that particular image set.

See Help > Testing Your Pipeline for more details. Hope this helps!