Bacteria image analysis: Migrating CP1 to CP2 and Align mod


We obtain phase contrast and fluorescence images of bacteria. From each spot we obtain 1 phase contrast and 1 corresponding fluorescence image. There are 12 spots per sample. We do timelaps series of those 12 spots.
If you look at the list of the filenames in excel sheet they go as 1,1,1,2,2,2,3,3,3,4,4,4 and then again 1,1,1,2,2,2 etc.
We need to count cells in those images. I think original pipeline was written for us by Mark a few years back.

I could not upload files so I combine them in one zip archive and placed in my dropbox public directory. …

I have a couple of questions.

Question1 is related to migration to CP2 from CP1
I’ve migrated the pipeline into CP2. Although it does run without errors, but image analysis is worse in newer version. I checked and I think I am using exactly same set of parameters. I’ve attached both pipelines and an excel file with my image file names. Also image subset is in the zip file - when running both pipelines on this subset you should see the difference.

Question2 is related to the use of Align module.
I would like to align the first phase contrast image 1 in the first time step with the first phase contrast image in the second timestep. See excel file with file names - excel rows A1 and A25, A3 and A27, A5 and A29) etc.
Then I would like to use the shift information from align module to shift fluorescence images.
See attached excel spreadsheet. Could not figure out how to do it.
When I did both green and orange fluorescence in the same cycle - I could align the phase contrast images, but I could not figure out how to use X and Y shift to align fluorescecne images from green and orange channels.

If you need more information - please, contact me.
Thank you

Hi Maxim,

I took a look at your pipelines; I think you made a mistake in translating it to CP 2.1. In the first Resize module, you have Orig1F as the input, when it should be Orig1P. Fix that, and it should work.