intensity profile data

[Kamilla]

hi everyone,

I am interested in collecting intensity profiles of my fluorescently-labelled bacteria and analyse signal distribution among their length. I managed to retrieve individual intensity profiles, however I am not sure how to get the data itself. Would also be helpful if anyone could suggest how to process them all together to get average intensity profile

[Oufti]

HI Kamilla,

Getting fluorescence intensities from the cell mesh is actually quite trivial. First, follow the fluorescent signal profile tutorial on the quickstart section of oufti.org. That will show you how to add signal fields to your cellList. Our web page also explains the format of the cellList. To get total or mean signal intensities, all you have to do is access that data structure. There is no complicated coding involved.

The signal for a cell can be accessed as:
cellList.meshdata{1}{1}.signal1

The only thing that you need to do in order to calculate average intensity profiles is loop through all of them to collect the data (in Matlab or any other coding language you prefer), normalize for both cell length and intensity, and then calculate the averages.

Thanks for using Oufti!

Op donderdag 14 maart 2024 om 17:12:19 UTC+1 schreef Kamilla: