How to measure blood flow velocity using two-photon microscopy?


I use line scan for blood flow imaging with two-photon microscopy in mouse. Has anyone dealt with this image with imageJ, MATLAB or other software? Thanks.

Blood flow/velocity measurement


Welcome to the Forum!

Would you be able to provide more specific information? What type of image is this exactly? What analysis are you interested in carrying out - ie. what are you interested in measuring?

The more details you can provide - the better we can assist you.

eta :slight_smile:


Thank you etarena. The abscissa axis represents the measured blood vessel, and the ordinate axis represents the 1000 times line scan of the measured blood vessel, which is equivalent to time course, and the slope of each line represents the direction of the blood flow. Five regions of the blood vessel were scanned. Blood flow velocity should be calculated as shown in the following figure, v=Δx /Δt. Does imageJ have something similar to this application?


Hi @Totoro_Xie

I have used the MATLAB-based software from Kim et al. succesfully for similar images of line scans. The link to the software can be found in the method section.


Thanks, aklemm. This paper you attached is very helpful, I also found the MATLAB code.