Hi Jasper thanks for the video!!!! how do you uncompress the videos in order to open it with ImageJ? because y use ffmpeg but when i open the video appears with colors changed and I cannot perform the analysis again thank you for the video
Hi, Dear Jesper, I have a problem, because I can not load 10 min videos in ImageJ. No even 2 min videos. It says that it is out of memory. I could use 64but machine, but there Quick time does not run. Do you know how to solve it? Thank you! Marcela
Hi Marcela, I just noticed your comment. I'm aware of the limitations in ImageJ under 32Bit and I assume you have already maximized the memory available for ImageJ in the settings. Have you tried using a Virtual Stack? The latest version of wrmtrack supports analysis of virtual stacks, but it doesn't give as many options for background removal. (see wrMTrck build101004 - on-the-fly analysis of virtual stacks)
Sorry this video was posted so long ago, but is still the only video out there on this software. I am having trouble with some steps before getting to the worm tracking. 1) How do you film the worms? Your example videos above have the worms very dark against a light background. I find the worms are unpigmented and so are very difficult to see. They are almost always out of focus and you can only fit one or two in a field of view and then they disappear very quickly out of the shot. 2) How do you get your video, eg I have some in a .wmv format into a format that wrmTrck can open? I hear that you have to use an uncompressed .avi format, but I cannot find anything that can convert to that, even the adobe suite of video production software can not make "uncompressed" .avi files. 3) How much footage do you need to be useful and what is an appropriate unbiased method of filming your plates? ie what are some examples of, and what would be an example of appropriate sampling when using this technique in an actual experiment to examine the effect of a particular treatment on worm movement? Sorry for the questions but I am finding it difficult to find explanations on exactly HOW to do anything when using c elegans. Thanks so much!
Dear Haydn Allbutt, I'll try to answer your questions: 1) I used an Orca R2 camera and a 10x stereo microscope. (see www.ncbi.nlm.nih.gov/pmc/articles/PMC4354510/ ). You do not need a lot of magnification - It sounds like you are using a microscope with too high magnification- The back lighting is relatively important to get good contrast. 2) There are a variety of video converters available - Moreover ImageJ has a lot of plugins that might help you to import different video formats. Maybe have a look at this page : www.wikihow.com/Convert-WMV-to-AVI . 3) This depends on how significant the differences you want to quantify are. I would typically have couple of movies with ~20 animals thrashing in a video and record 30 seconds of footage 672x512 pixels@23.53fps per condition - this was just under 1GB so it could be loaded into imageJ on a 32bit machine. I hope this helps Cheers, Jesper
Hi Mr. Pedersen! I was just wondering if we could use Image J in tracking the motion of Ascaris suum. And if yes, what type of agar should be used? Thank you so much!!Looking forward for your reply.
The plates we used are standard NGM plates (www.wormbook.org/chapters/www_strainmaintain/strainmaintain.html) We flood the plates with M9 to induce the swimming behavior. I do not now if this works for Ascaris suum - I have no experience with this species...
Hi! I've been following the steps said here and all is going well until I use the wrMTrck plugin. I set the threshold as instructed but the worms are not labeled, hence there are no results. Does anyone have the same experience and how did you troubleshoot it? Thanks a lot!
amazing. That's what i needed
Thank you very much
Hi! Great video and plugin. The sound of the video maybe is a bit strident
Thanks! That helps me a lot.
Would you be able to track insects in water and quickly count them?
Hi Jasper
thanks for the video!!!!
how do you uncompress the videos in order to open it with ImageJ? because y use ffmpeg but when i open the video appears with colors changed and I cannot perform the analysis
again thank you for the video
Hi, Dear Jesper,
I have a problem, because I can not load 10 min videos in ImageJ.
No even 2 min videos.
It says that it is out of memory. I could use 64but machine, but there Quick time does not run.
Do you know how to solve it?
Thank you!
Marcela
Hi Marcela, I just noticed your comment. I'm aware of the limitations in ImageJ under 32Bit and I assume you have already maximized the memory available for ImageJ in the settings. Have you tried using a Virtual Stack? The latest version of wrmtrack supports analysis of virtual stacks, but it doesn't give as many options for background removal. (see wrMTrck build101004 - on-the-fly analysis of virtual stacks)
How do you determine the pixel size of a worm?
Sorry this video was posted so long ago, but is still the only video out there on this software. I am having trouble with some steps before getting to the worm tracking. 1) How do you film the worms? Your example videos above have the worms very dark against a light background. I find the worms are unpigmented and so are very difficult to see. They are almost always out of focus and you can only fit one or two in a field of view and then they disappear very quickly out of the shot. 2) How do you get your video, eg I have some in a .wmv format into a format that wrmTrck can open? I hear that you have to use an uncompressed .avi format, but I cannot find anything that can convert to that, even the adobe suite of video production software can not make "uncompressed" .avi files. 3) How much footage do you need to be useful and what is an appropriate unbiased method of filming your plates? ie what are some examples of, and what would be an example of appropriate sampling when using this technique in an actual experiment to examine the effect of a particular treatment on worm movement? Sorry for the questions but I am finding it difficult to find explanations on exactly HOW to do anything when using c elegans. Thanks so much!
Dear Haydn Allbutt,
I'll try to answer your questions:
1) I used an Orca R2 camera and a 10x stereo microscope. (see www.ncbi.nlm.nih.gov/pmc/articles/PMC4354510/ ). You do not need a lot of magnification - It sounds like you are using a microscope with too high magnification- The back lighting is relatively important to get good contrast.
2) There are a variety of video converters available - Moreover ImageJ has a lot of plugins that might help you to import different video formats. Maybe have a look at this page : www.wikihow.com/Convert-WMV-to-AVI .
3) This depends on how significant the differences you want to quantify are. I would typically have couple of movies with ~20 animals thrashing in a video and record 30 seconds of footage 672x512 pixels@23.53fps per condition - this was just under 1GB so it could be loaded into imageJ on a 32bit machine.
I hope this helps
Cheers,
Jesper
Hi Mr. Pedersen! I was just wondering if we could use Image J in tracking the motion of Ascaris suum. And if yes, what type of agar should be used? Thank you so much!!Looking forward for your reply.
Give it a try. I know people have been using my plugin to track everything from cells to fish.
May I ask what type of agar have you used in C. elegans?
The plates we used are standard NGM plates (www.wormbook.org/chapters/www_strainmaintain/strainmaintain.html)
We flood the plates with M9 to induce the swimming behavior.
I do not now if this works for Ascaris suum - I have no experience with this species...
Hi! I've been following the steps said here and all is going well until I use the wrMTrck plugin. I set the threshold as instructed but the worms are not labeled, hence there are no results. Does anyone have the same experience and how did you troubleshoot it? Thanks a lot!
Have you adjusted the minimum and maximum size of objects tracked?