Tracking of moving particles (micromotors) using FiJi or ImageJ
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- Опубликовано: 9 сен 2024
- Here is a quick tutorial for tracking the motion of moving particles (micromotors etc.) for the determination of their speeds (um/s). You will need the resolution of your video camera (pixels/um) to be able to do this.
CORRECTION: In the video, Time Interval is the amount of time between adjacent frames. I made a mistake by using the total clip during for this field. Thanks to Sakhawat Shah for point this out.
Thanks a lot bro! This video is amazing!
Very interesting video..Thanks Safdar!
thanks a lot for this video! you should make more tutorials!
Hi, Thanks for the video. I have a few questions. Kindly help me out.
I'm unable to understand the x/y calibration. Is it like camera property? Can we retrieve that information from the video clip? Currently, I have a video clip of 6s, 1072*1072 pixels. The clip was taken using Zeiss LSM 780 confocal microscope.
Hi, Thanks for the question. The x/y calibration refers to the “pixel size”, (precisely, pixel distance) for calculating a velocity for in µm/sec. Take a look at this article which may be helpful. forum.image.sc/t/tracking-cells-using-imagej/595
You have to see the zoom of your objective and the pixel size of your camera. For example : your camera has pixel size: 16µm, and you use 63 x obj. your image in 1 pixel = 16/63 µm.
Thank you!
video is good, u should make the next tutorials with a louder voice, here it seems u r talking yourself, cant be heard well. but the video description was very good.
Hi, sorry for that. It was my first video that I created ever, so I had a lack of experience. Didn't pay much attention to the sound.
I don't understand why for the velocity you just sum up all the velocities, why not take the average?
Average will give you wrong numbers. The tracking is frame-by-frame, and for a total 50 frames you will have yo sum it, not average.
@@1400740 I don't get the point! I mean, how can the overall velocity during a path be the sum of the instantaneous velocities during that path? Help me understanding pls 😂 if I walk 1 seconf at 1m/s and then another 1 second at 2m/s my overall velocity is not 3 m/s
I was having the same question in mind... I'm sure Safdar has his point of view, but I'm sorry I couldn't understand it as well, which makes me stick with Simone's doubt... if the given value is already velocity taken from two frames... shouldn't we get an average value of those velocities for given range of frames? I hope you can clarify this doubt for us Safdar.. Thanks a million!
Hi Simone, recently I have verified that the sum of the velocities in the column is the average velocity of the given frames, Safdar is right, it can be easily proved by adding the total distance travelled by the particle divided by the time used. Indeed, the value calculated is similar to the sum of velocities. The question of yours, "why not take the average?", can be explained by defining the velocities in the velocity column as [distance travelled by the particle between two frames (micrometer)/ total time used for the complete track from first frame to the last (s)]. That's why the sum of these velocities will be the total distance travelled by the particle divided by the total time used for complete tracking. Hope it answers your doubt and have a nice day!
It is because the time interval is here improperly defined. In order to compute the instantaneous velocity, you have to divide by the interval of time between two frame, not by the total duration of the film made of N+1 images. So the instantaneous velocity in this video are false by a factor of 1/N.
This explains why when Sadfar sums the N+1 values he got for the velocity, he miraculously recovers the good value for the average velocity ...
Hi, it is possible to track multiple objects using this plug in? thank you
Unfortunately not, because it is a manual tracking method so you can track only one object at a time.
Hi, thank you for your good video tutorial! I have an easy question. after saving the tracking table data with the button "Load Previous Tracking File", when I reloaded the data, the table just showed zero-values. Do you know any solution about this problem?
Hi, sorry but why should you load the table with "Load Previous Tracking File"? if you need to do the calculation, open the data file in excel.
@@1400740 just for continuing the tracking work with previous tracking data when I did not finish all of the tracking work at once. :)
@@sungshilkim Better you do the tracking in one go. You should use short clips (5-10s long). It shouldn't be a problem to finish it in one go.
@@1400740 Sorry. my image sequence has lots of particles and I just want to record all of the tracking information in one csv file. Thanks for you reply anyway!
@@sungshilkim In such a case, auto-tracing is a better option. It more complex but does track several objects simultaneously. I never used it though. Good luck
The tutorial is really good. I didn't get how the dots are overlaying in the video
Thanks. If you are refering to the blue line, it is drawn by the software by connecting the coordinates you clicked while tracking the moving particle.
Hi, I've got this polymer that was placed in solvent and it keeps swelling, I took images at different time intervals. Please can anyone help on how I can use Fiji (ImageJ) to analyse the change in size of the polymer for all the different images captured.
Hi.. did you figure it out how to analysis.. if it is can you help me out
Thanks for an excellent video. I think the time interval you put 42 isn't correct. I think it's interval b/w frames, Like I have 17FPS video.. so it give me time interval of 0.062 sec.
Also, would you more explain about x/y calibration? I took images, 17 fps, 50 um, 10X lens, the microscope showed 0.29um/pixel @ 4908*3264.
Thanks for the correction. Time Interval is the amount of time between adjacent frames. ‘x/y calibration’ is the number of your unit distance per pixel (the inverse of the number of pixels per unit distance).
Hi! thanks for you video, I have a little problem. I have Fiji installed in my Mac, when I upload it to Fiji it appears a window that says BIO-FORMATS IMPORT OPTIONS and I don't know what I should click or move.. and if I leave it as normal it doesnt load my video it says that maybe its not a supported format, the reader plugin is not available or it was not found. the format of my video is .MOV
Do you know what can I do or how can I change this???
thanks!!
I am pretty sure that .MOV video format is not supported by FiJi for tracking purpose. If I may remember correctly, its the .AVI format that I used in this video.
@@1400740 thats what I thought but I also changed the format to .AVI and it still appears like its not supported :(
Fatima Lara Yes, because the .mov to .avi conversion does not work as the file is already compressed due to the mov format. You must use a camera that records the clips in .avi or other uncompressed formats.
Thanks for the video! I have a question regarding to the definition of 'time interval', is it the total time or the time between two adjacent images?
Total interval of the clip.
hi Safdar, i have the problem about fiji cannot read my .mp4 file, what is your version of imageJ that you used?
Hi. It is possible that the file that you are trying to open is compressed. Most mp4 files are compressed. Fiji can only read uncompressed (like .avi) files.
You can download a decoder. I had the same problem but found a way to open the videos. I have a video on how to fix that.
Hi Safadr, is it possible to measure velocity of a particle if it is moving back and forth by ImageJ. (Ex.contraction and relaxation )
Hi Aviseka, should be no problem imo.
Hey :) Thank you so much for your reply . I would request to teach me how to measure it . I do have the video with me. can you please help me out :)
Regards
Avi
it will be great if can let me know the possibilities.
@@acharyaaviseka85 Sorry, I just noticed your response now. Did you manage to do it? You may have to first track your particle during the contraction, and then during the relaxation. You will get two kinds of velocities in this manner. I have never done such thing so I can't help much.
Time inverval is the total time??? Wtf
Please read the description. Here is it. CORRECTION: In the video, Time Interval is the amount of time between two frames. I made a mistake by using the total clip time.
Which plugin is needed to be downloaded to get the tracking option in image j Plugin Option?
No additional plugins needed. Its already in default imageJ.
@@1400740 probably it's available in Fiji application because it's not there in the default ImageJ application
@@oyster2334 Yes, plz try Fiji.
I remember I have used in ImageJ as well. But Fiji is better.
@@1400740 okay thank you so much Sir
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