Timeseries of fluorescence of 3D biofim

Thanks, I was able to get this working. Paraview is quite cool with 3D data but it seems most of the functionalities stops working if your data is in 2D. Do you prefer Paraview for 2D data too?
Secondly, If I get cubes of biofilms after segmentation of the stack, which of the data parameters should I select in the output to get a time-series of the fluorescence biofilm.

Hi Emmanuel,

welcome to the image.sc forum!

Do you prefer Paraview for 2D data too?

The sole purpose of ParaView is the rendering of 3D data to check and visualize the BiofilmQ analysis results. 2D data analysis can be visualized in 2D (or sometimes 3D) with the built-in visualization functions. (i.e. the preview function or the plotting functions).

Secondly, If I get cubes of biofilms after segmentation of the stack, which of the data parameters should I select in the output to get a time-series of the fluorescence biofilm.

The choice of the right parameter if basically an open field and depends heavily on your research question. If you give me a little background on your question, I might be able to give a recommendation:

I.e. if you have two constitutive reporter strains and want to quantify the total growth difference, the global biofilm volume is the parameter you are looking for.

In contrast, if you have a fluorescent reporter which signals gene expression, you are probably more interested in the fluorescence properties throughout the biofilm.

As I said, it really depends on your research question, and I need a little more context here in the forum to help you with this.

Best wishes,

Eric

Hi Eric

Thank you so much. In my research, I have fluorescent reporter which glows stochastically in bacteria over time. After the lifetime imaging, I can plot the fluorescence over time for a single bacterial. However I am interested in measuring the fluorescent signal over time in biofilms.

So yes, I am more interested in the fluorescent properties throughout the biofilm as you said. Which of the parameters in biofilmQ is best for this. There are different parameters in the ‘fluorescent properties tutorial’

If you are only interested in the overall fluorescence in your sample, I would just use Intensity_Mean.

However, I strongly suggest to use a second (constitutive) reporter for the segmentation step. This would enable you to measure the fluorescence over time in relation to the biovolume of the sample.