IdentifyObjectsManually -SavingObjectsFor Subsequent Analysis


Is there a way to save the objects from the IdentifyObjectsManually Module so if you want to run a subsequent analysis on the objects you don’t have to manually identify them again?

Thanks very much, any help much appreciated.


Hi @Randy_Strauss,

Yes. You can do that. After the “IdendifyObjectsManually”, you can convert the objects to image using “ConvertObjectsToImage” module. You can convert it into binary image or other image type to by choosing the appropriate option. This converted image could also be saved using “SaveImages” module & use it later in the other pipeline or other softwares.
In case you want use it in the same pipeline, you can use “MaskObjects” module & do any analysis inside or outside the mask.
Hope this helps.

Fujifilm Wako Automation (Consultant)
For CellProfiler training or optimised pipeline write to,

Read more on our site.
Yokogawa CV8000 - The Ultimate in Confocal HCS

Hey Thank you this was very helpful.

However, here’s what I’m trying to do:

I have Z stack images of 40 slices per stack. I want to measure the intensity of a fluor at each slice but only within the objects that I create from that Z stack’s maximum projection image.

How to ensure that that max projection based objects that I create will be applied to the appropriate Z stack etc.???

Thanks very much!

This is definitely doable- you just need to match the manual objects you created to each frame of your original Z stack.

This is possible by using CellProfiler’s Metadata-based matching in NamesAndTypes; here is one example where someone was doing that to identify objects in one time point of a movie, then measure them across all other timepoints. The exact same concept applies to Z stacks, because ultimately CellProfiler doesn’t care about whether you’re analyzing different Z’s or T’s, all CellProfiler cares about is "for some of your image sets, you get a new image every time (in your case, your individual Z planes), and for some you reuse the same image over in over (in your case, your manually drawn objects). You can find more help for that in the “Image set matching method” section of the help for the NamesAndTypes module. Good luck!