search

wiggins-lab / SuperSegger

A completely automated MATLAB-based trainable image cell segmentation, fluorescence quantification and analysis suite, particularly well suited for high-throughput time lapse fluorescence microscopy of in vivo bacterial cells.
GNU General Public License v3.0
32 stars 20 forks source link

Info about generation #17

Closed RoxaneMo closed 6 years ago

RoxaneMo commented 6 years ago

Hello,

Where can I find information about number of generation? I want to know for each cell if it belongs to the first, second, third generation... I saw information about the age of the old pole but what I would like to know is the generation of the cells regardless the time they took to divide.

Thank you. Roxane

pawiggins commented 6 years ago

Hey Roxane:

That information doesn't exist yet but would be easy to compute. Next time I edit the code, I will add that feature in the clist.

But for now... load up the clist. For cells that don't have mothers, set generation 0. For cells with mothers in generation 0, set generation 1, etc.

I would use the MATLAB builtin function ismember.

--PAW

RoxaneMo commented 6 years ago

Hello,

Thanks for your answer that helped me. Instead of starting with cells that don't have mothers, I started with cells that have "Cell birth time"=1 because I don't consider cells that I cannot follow the genealogy from the first frame.

Roxane

pawiggins commented 6 years ago

Yeah....I agree that for many applications, this is what you want.

Sent from my iPhone

On Jul 18, 2018, at 8:02 AM, RoxaneMo notifications@github.com wrote:

Hello,

Thanks for your answer that helped me. Instead of starting with cells that don't have mothers, I started with cells that have "Cell birth time"=1 because I don't consider cells that I cannot follow the genealogy from the first frame.

Roxane

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

pawiggins commented 6 years ago

Roxane:

This is now in the clist.

--PAW