Feature comparison of mac vs pc CellProfilerAnalyst versions

Will the PC version support brushing, cross validation, and parallel coordinate plots like the mac version shown in the CellProfiler Analyst demo movies? I was wondering if I should get a mac or is the pc version going to have the same features in a future release?

As we add features, we intend to make it available in both PC and Mac versions simultaneously. As you’ve seen, cross-validation is available, brushing is in the works, but parallel coordinate plots is not one that we have heard much feedback on. Is it something you would use?


I think brushing would be my most desired feature that is not in the current CPAnalyst 2 release. We are only using CellProfiler for frozen tissue sections, so, I would like to find a way to filter the stromal and immune cells’ contribution to the histogram and scatter plots. I found another comment on this forum discussing mysql sorting by class assignment that could probably do something very similar, but I usually use the sqlite database for measurement data output. So, the mysql database filtering option probably will not work with sqlite. Do you plan to implement a way to select a sub-population of cells in the scatter plot that can bring up the corresponding marked cells in the image that the data originated from? That is my second most desired feature. I think that the parallel coordinates plot would be an excellent tool for looking at the relationship of the most important classification rules found by the classifier. Thanks for developing such a great image processing/analysis software package.


As it is right now, you can select a sub-population of per-image/per-object points, right click to bring up a context menu and then bring up the images that the points came from (or a list of the images), which you may be aware of already. But with the currently released version, the selected objects are not marked if per-object is used. This has been on our to-do list to implement.

Have you seen the “Check progress” button in Classifier? It allows you to see the relative importance of each rule in regards to your training set. There is a thread referencing this feature here.


I think that the scatterplot function would be significantly enhanced by implementing a color datapoints by class option. An interactive brushing data point selection method that links a histogram plot or parallel coordinates plot will be a great analysis tool addition for future CellProfiler Analyst 2 software releases.