Thank you for this video, I finally have a good FRAP recovery graph! For the people asking how to change Tau to time, I followed all steps however to get time on the x axis, I initially opened all FRAP images as plot Z axis, then combined trajectories and followed the same procedure as the video. I do have a question though, do you know how to change the axis values for a nicer looking plot? At the moment my x axis values are at 26.67, 53.33, and 80 (set as max value) but I'd like these to be more even intervals such as 10 secs etc. I have googled for ages but I cannot find an answer. I appreciate this is an old upload now. Thank you :)
Hi Jasmine, unfortunately this isn’t possible in Fiji. You can click the “list” button on the pw2 window which will give you a csv-type sheet that you can either save as csv to load to another program or copy to another program to replot as you see fit. If you decide to do this, you can get your X-axis on a time scale by multiplying the frame numbers by the time interval. Thank you for your question!
Thanks for your great video. Regarding the parameters obtained by curve fitting, is it possible to get the half-recovery time here? or, does tau indicates this time?
Hi Osamu, Tau indicates something close to the half-recovery time. Tau is a fit parameter from the exponential function which indicates it’s characteristic recovery rate. The half-recovery time is usually close to the same value, but is not a fit parameter from a true mathematical function fit to the data. These steps will report only tau, you’ll have to calculate the half-recovery time manually. Thank you for your question!
@@StowersInstitute Thany you very much for your kindly reply. I understood tau value is close to half-recovery time, but it is necessary to calculate the half-recovery time manually. I will try to calculate the time by myself.
It’s hard to know exactly what is happening. First, check to make sure your plugins are up to date. You can do this following the instructions in video 1 of this series. If that doesn’t help, simplify things and make sure your data has only one channel and one z slice with many time points. The combination of these things should fix the issues you’re having.
Thanks for nice video. How do you handle control (unbleached) ROIs? The same as bleached ROIs? I have another question: Is there a way to import ROIs in ImageJ automatically? Because I have many ROIs in each cell and everytime I have to look on the original images in ZEN software to remember all ROIs...
Thanks! Yes treat your unbleached control the same as your bleached samples. Make sure to sample from the appropriate region of the sample as you did in the bleached samples. I haven’t spent much time trying to import ROIs so I don’t know of a direct way to do this. -- Jeff Lange
The tau value you get from the fit will be in frames. To convert to time, you’ll need to know how often you collected data. Multiply the tau (frames) by the frame rate (time units per frame) to get the tau value in units of time.
You have a few options. The first is to just drag and drop multiple .pw2 files onto the Fiji toolbar, this should normally work. If it doesn’t you can try dragging and dropping them onto the “Bio-Formats Plugins Shortcut Window”. This should also work. If it does not there is likely something wrong with Fiji. We can try to fix it in two ways. One by running a plugin called “register jay readers jru v1”. This may correct the issue. If not, finally update the Stowers plugins through the “Help - Update” path like in the first video of the series.
Awesome video! Super easy functioning plugins, thanks for sharing good science practice!
Very clear tutorial! Thanks :)
Thank you for this video, I finally have a good FRAP recovery graph! For the people asking how to change Tau to time, I followed all steps however to get time on the x axis, I initially opened all FRAP images as plot Z axis, then combined trajectories and followed the same procedure as the video.
I do have a question though, do you know how to change the axis values for a nicer looking plot? At the moment my x axis values are at 26.67, 53.33, and 80 (set as max value) but I'd like these to be more even intervals such as 10 secs etc. I have googled for ages but I cannot find an answer. I appreciate this is an old upload now.
Thank you :)
Hi Jasmine, unfortunately this isn’t possible in Fiji. You can click the “list” button on the pw2 window which will give you a csv-type sheet that you can either save as csv to load to another program or copy to another program to replot as you see fit. If you decide to do this, you can get your X-axis on a time scale by multiplying the frame numbers by the time interval. Thank you for your question!
Thanks for your great video. Regarding the parameters obtained by curve fitting, is it possible to get the half-recovery time here? or, does tau indicates this time?
Hi Osamu, Tau indicates something close to the half-recovery time. Tau is a fit parameter from the exponential function which indicates it’s characteristic recovery rate. The half-recovery time is usually close to the same value, but is not a fit parameter from a true mathematical function fit to the data. These steps will report only tau, you’ll have to calculate the half-recovery time manually. Thank you for your question!
@@StowersInstitute Thany you very much for your kindly reply. I understood tau value is close to half-recovery time, but it is necessary to calculate the half-recovery time manually. I will try to calculate the time by myself.
Thanks for the nice video. In my case, the plugin is not working for creating spectrum? Can you please help me
It’s hard to know exactly what is happening. First, check to make sure your plugins are up to date. You can do this following the instructions in video 1 of this series. If that doesn’t help, simplify things and make sure your data has only one channel and one z slice with many time points. The combination of these things should fix the issues you’re having.
@@StowersInstitute sir can you please share the video 1 link ?
@@user-pj6wq6fm4m th-cam.com/video/4CkRX1KPaCs/w-d-xo.html
Thanks for nice video. How do you handle control (unbleached) ROIs? The same as bleached ROIs? I have another question: Is there a way to import ROIs in ImageJ automatically? Because I have many ROIs in each cell and everytime I have to look on the original images in ZEN software to remember all ROIs...
Thanks! Yes treat your unbleached control the same as your bleached samples. Make sure to sample from the appropriate region of the sample as you did in the bleached samples. I haven’t spent much time trying to import ROIs so I don’t know of a direct way to do this. -- Jeff Lange
Great video, how do you change your Tau to time?
The tau value you get from the fit will be in frames. To convert to time, you’ll need to know how often you collected data. Multiply the tau (frames) by the frame rate (time units per frame) to get the tau value in units of time.
Hi. This is a life saver. I am not able to run any of those plugins. Do I need to install those separately? If yes, how?
Thanks
Check out Part 1 of this series, which explains how to install the plugins.
is it possible to convert from into time
how i determine half of recovery from tau valu
How do I open multiple pw2 files together? Right now, I can only open it one at a time using import trajectory.
You have a few options. The first is to just drag and drop multiple .pw2 files onto the Fiji toolbar, this should normally work. If it doesn’t you can try dragging and dropping them onto the “Bio-Formats Plugins Shortcut Window”. This should also work. If it does not there is likely something wrong with Fiji. We can try to fix it in two ways. One by running a plugin called “register jay readers jru v1”. This may correct the issue. If not, finally update the Stowers plugins through the “Help - Update” path like in the first video of the series.