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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
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Growth Rate #23

Open RoxaneMo opened 5 years ago

RoxaneMo commented 5 years ago

Hello,

I have some questions about the Growth Rate information in the clist.

How is it measured? (units?) If a cell does not divide anymore, what is the value? NaN or 0? I saw negatives values as well and I do not understand them.

Thank you. Regards.

Roxane Moritz

pawiggins commented 5 years ago

Hey Roxane:

You can see the formula at line 380 of trackOptiClist.m

rate = log(L(t))-log(L(0))/t

so this is the cell elongation rate:

k = dL/dt/L

which would be in inverse frames. If the cell is shorter than the initial length (noise or biology), the value would be negative. We do observe cells getting shorter when stressed. These would have a statistically-significant negative rate.

—PAW

On Oct 25, 2018, at 6:04 AM, RoxaneMo notifications@github.com wrote:

Hello,

I have some questions about the Growth Rate information in the clist.

How is it measured? (units?) If a cell does not divide anymore, what is the value? NaN or 0? I saw negatives values as well and I do not understand them.

Thank you. Regards.

Roxane Moritz

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