Quantification* of *fluorescence intensity* of labeled neurons.

[Pablo Munoz-2]

Hello
I writing because I really really need help with the *Quantification*
of *fluorescence intensity* of labeled neurons.
I am interested in measure the fluorescence intensity along to the axon or
neurites of neurons, and measure a protein in the tip of the axon, but I
dont know how to do it and the plugins like neurite
tracer and NeuronJ does not have a  option to that measure.
If some can help I would really appreciated.

I hope you can help me

Best Regards

Pablo

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[Danny Misiak]

Dear Pablo,

I developed an algorithm to detect single cell neurons in a multi-channel fluorescence image. The neuron is completely segmented and each single neurite is detected and separated from the soma. After segmentation a protein profile for each labeled protein is extracted along the neurite from the origin to the growth cone. My algorithm is actually working on single cells, but will be adapted for multi-cell analysis. Currently I worked only on primary hippocampal neurons. In the near future the algorithm will be available at the microscope image analysis toolbox - MiToBo (www.informatik.uni-halle.de/mitobo).

If you are interested in the algorithm you could send me an example image to test whether the algorithm is able to quantify your neurons.

Kind regards, Danny.

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[Pablo Munoz-2]

Hello Dany

thank you for your answer that can help to analyze the neurons, I will send you   one picture explaining what I want to measure. So then if it is possible you can help me with your algorithm.

Thanks again for your help.

Pablo

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[repnick]

Hi Danny,

I have little experience programming but am wondering if your algorithm can help me out with a somewhat specific project. I am trying to measure the length of the Axon Initial Segment (stained with ankyrin G) and its distance away from the soma. To determine the beginning and end of the AIS, the program must be able to find where the intensity of the axon crosses an arbitrary threshold. It must also determine the end of the axon and the beginning of the soma, which could be done by taking the average intensity across sections perpendicular to the axon. Here are sample images of what I would need analyzed:

Stain of the axon and soma: http://i.imgur.com/clxB3oE.jpg
Stain of the AIS: http://i.imgur.com/j6Iz2AB.jpg

If you think your algorithm would be useful, please let me know.

Thanks

Nick