The CellProfiler 2 User's Guide to CellProfiler 3.0, Part I: Using the new Test Mode


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Everyone here at the CellProfiler team is very excited about our new 3.0 release, and we certainly hope you are too! CellProfiler 3.0 is much faster than any of our previous releases, and the addition of volumetric processing is a huge game changer.

CellProfiler 3.0 looks pretty similar to what you’re used to, albeit a bit sleeker than previous versions. While most of it still behaves exactly how you’re used to from using different CellProfiler 2 versions, the biggest change involves running pipelines in Test Mode- you’ll notice the (beloved or hated, depending on who you ask) slider has not made the jump to 3.0. Instead we’ve gone the much more streamlined route of using the module list itself to indicate where you are in the pipeline- the module you’re currently looking at is highlighted and has its name in bold type. If you’re jumping around through modules and not sure how much of the pipeline you’ve run so far, never fear about forgetting where your place is either- we’ve also shaded in and underlined the next module that will run when you hit “Run” or “Step”.

If you want to rerun from a certain step, we’ve kept the ability to do that too; simply go to the module you want to run from and right-click, and you’ll get an option to “Run from module #”.

Questions or comments about the new test mode? Please let us know below!