Wormies,
Can anyone give me feedback on the MBF WormLab program vs. other worm trackers? I read the very helpful WormBook chapter on worm trackers, but it does not go into much detail about the relative merits of the (expensive) MBF WormLab program. I have a lab with mostly undergraduates; we all have very limited computer skills. Ideally, I would like my students to be able to compute the average velocity of large numbers of worms and also be able to analyze the behavior of individual worms (outline) without using a X-Y stage control. Current thoughts are to try and do this with a combination of Nemo (Taverarakis Lab) and the Parallel Worm Tracker (Goodman Lab). But if the MBF system is a lot easier to set up, it might be worth the $5000 to get the students up and running. I would appreciate your thoughts.
Janet Duerr, Ohio University
Hey Janet,
You can try it for free for 30 days, and I think it is more than enough time to do the activity in the lab. Actually the output is given in 2 ways. One way is they give the velocity of each tracked worm at each time frame. There are three types of speeds outputted (speed, moving average speed, and smoothed speed). The other output comes in a summary table that includes speed and other endpoints.
So, there is not much calculation work done by the students.
For the raw data, it is ALOT. so excel experience might be helpful in dealing with it.
Also, the speeds given don’t specify if they are for forward or backward…
Note: If you have a lot of tracked worms per video, it takes a lot of time to analyze, and it freezes too. So I suggest you can put 20 worms per plate, and then track 5 to 10 worms only per video analysis.
One thing to keep in mind is, the software sometimes switches head and tail. So in case you care about number of reversals, or forward versus backward speed, this might be an issue because a 5 minute video with about 20 worms might take 1-3 hours (if computer is a bit old, it even takes more time) just for analysis. You can figure out a way to detect those worms via excel/calculations and remove them from reversals or forward/backward speed calculations.
I think yes it might have some flaws, however, I have tried other software and they were not that good. I did get some useful data from it, and it is easy to operate by undergrads. Actually it gives around 10 endpoints and a summary.
But another thing is, when you buy the license, it is for one computer only. Then you can buy one on USB for 500$ for another computer.
You can only save a limited number of videos on the computer (I believe 10 max). So, usually I export the data to excel file. The down part is, if for some reason one forgets to export one endpoint, the whole analysis should be repeated and then better off in using all newly outputted endpoint values for consistency. (in case one is working with a lot of videos, that is just too much time:( ).
I hope this helps a bit.
Best,
Faten
Hi Janet,
I guess it depends upon how much sophistication you want in your tracking system. For an undergraduate class where they would be doing a combination of number crunching and observational skills, then you could probably get away with spending nothing if you already have low power microscopes and video/cmos cameras.
For example, wrMTrck is a plugin for ImageJ and does a fairly good job of generating basic information about multiple worm velocity and movement characteristics. The advantage is that both wrMTrck and ImageJ are free and have great support;
http://www.phage.dk/plugins/download/wrMTrck.pdf
The main issue (and this goes for lots of basic and sophisticated software too) is the quality of the starting video. The pdf above gives a very good summary of the most important points for the students to consider, which I think is also an important part of the learning process.
With large numbers of worms one has to be aware that tracking software will often treat tracked worms crossing over other worms as a new ‘entity’. So the students need to look at the video and check that new instances of tracked worms are not just the same worm being detected multiple times!
So, I would say that for an undergrad class it’s possible to keep it simple, informative and cheap.
Regards
Steve
Steve and Faten,
Thanks for the very detailed and helpful advice. Sounds like buying a better camera and an up-to-date computer would be a good idea to improve the quality and quantity of the data we can collect (I have a bit of year-end $ available). And I guess nothing beats playing with the software itself to know what it does.
I and my students have done a bit with Image J and WormTracker to analyze maximum velocity, but I was hoping that I could find “easy” software that would measure body posture, as well as forward and backwards velocities. Sounds like the MBF system is more user friendly, but still designed to measure velocities and not postures. So perhaps I will need to use ImageJ/Wormtracker (or MBF) and also MatLab with Nemo.
Again - thanks for the help - wormies are awesome!
Janet
I would give a look at Rex Kerr’s Multiple Wormtracker. It’s free on sourceforge. The software requires National Instruments Lab view components to run, but they are not that expensive (~$400) and many universities have site licenses, making it completely free (to me at least). For cameras you can actually get away with a web cam mounted on top of the petri dish on top of a light table. I’ve built multiplex imaging arrays for parallel worm tracking and each unit costs only a few dollars (you can get webcams for ~$5 on Amazon).
Hi Janet,
I would like to clarify some of what WormLab provides. Our company (MBF Bioscience) makes WormLab.
WormLab v2.2 outputs metrics for worm postures as well as position, speed and direction. It does this for each frame in the video, and also provide track summaries.
Some of the data available include:
position of points along the body centerline
bending angles along the centerline
worm body length
worm body mean width
wavelength
direction
The data analyses (like smoothed speed) are generated from the primitive data of the worm posture and position, which can be saved to the worm project file.
There is no limit to the number of saves during the trial period.
If you have more questions or need more information on WormLab, you can contact me or visit the mbf website. Just google WormLab and MBF.
I hope this information helps,
Jeff Sprenger
Vice President
MBF Bioscience