Automated Analysis of C. elegans Swim Behavior Using CeleST Software

An efficient and simple methodology for computer-based analysis of nematode swimming behavior in liquid is described. The method requires little to no investment for C. elegans laboratories. The hardware used is standard, and the computer software for the behavioral analysis (CeleST) is an open source one.

Transcript

The overall goal of this methodology is to quantitatively evaluate C.Elegans swim behavior using Computer Vision software called CeleST, for C.Elegans Swim Test"This analysis method can help address the impact of genetic mutations or pharmacological interventions on C.elegans swim behavior. It can also easily score the age-associated decline in locomotive capacities. The main advantages of this technique are that multiple animals can be tracked simultaneously, with different aspects of swim posture analyzed to score eight parameters of swim behavior, and automated data evaluation.

Begin by obtaining a stereo microscope and digital CCD camera as well as a computer with digital video recording software and computer vision software for the C.Elegans swim behavior analysis. Within the digital video recording software set up the following settings:Cover the microscope with a dark cloth to prevent glare in the swim drop area on the microscope slide, and improve image quality. Adjust the microscope's working distance and magnification to full view of the swim area, and adjust the base mirror to get sharp contrast of the animals against the background.

Then, set the illumination to dark field to visualize the bodies of the adults as white against a black background. Next, pipette 60 microliters of 1 x M9 buffer into a 10 millimeter ring, pre-printed on a microscope slide, and ensure the drop entirely covers the inside area of the ring. Transfer four adult nematodes into the drop of 1 x M9 buffer while minimizing the transport of bacteria that can cloud the liquid.

Minimize bacteria in the swim well by either allowing nematodes to crawl briefly on an unseated region of the plate before being transferred, or mixing the swim well slightly to disperse minor bacteria traces before recording. Next, position the slide loaded with adult nematodes on the base of the microscope to record their swimming behavior in liquid in 30 second videos. To record, select New Sequence in RAM under the Home heading, then press the red record button.

Finally, after recording is complete, click the Home heading and select Export Full Sequence, in order to fragment the video into a sequence of image frames. Begin by launching the Computer Vision software for C.elegans swim behavior analysis from Mat Lab by clicking the Run button. On the home screen of the swim analysis program, use the Add one video"or Add multiple videos"buttons to upload sequences of image frames one at a time or in groups while attaching relevant labels, such as genotype, date, trial, and duration.

Then, click Process videos"to enable simultaneous tracking of multiple animals in the uploaded sequences. In the new screen that appears, select the desired videos in the left box and click Add to the list"Next, demarcate the swim zone by selecting three points inside the ring and initiate processing by clicking Process all the videos listed above. View progress of the video processing at the center bottom of the screen.

After it has completed, close the video processing screen. Begin by clicking on Compute measures"to open a new screen where the processed videos can be uploaded one at a time to validate or reject the tracking of single animals. Use this manual step to focus on areas of missed tracking, shown in the red blocks, and contrast to successful tracking, noted in the green blocks.

Find the Validity of the segmented body"in the first color bar across the screen in the bottom half. Note the percentage of valid frames is in green, and the percentage of rejected frames is in red. Then, navigate and modify blocks of valid or rejected frames utilizing the next block, Switch validity"Split block"and Isolate frame"options.

In the rare event that two animals cross paths in an uncrowded swim zone, switch their identification numbers over a specific frame range with the Switch"button. Finally, click on Save and compute measures"to save the validity input before uploading another processed video. Then select Close"to exit the Compute Measures screen.

Note that the software computes curvature maps of the swim performance of individual animals in the background as well as the eight parameters indicated later. On the Home Screen of the Computer Vision software program, click Display results"to obtain the analysis output. Then, create sample groups for statistical treatment by selecting the desired analyzed sequences of frames in the left box and moving them into a newer existing sample group by clicking the Add to the selected sample"or Add to a new sample"buttons.

Click Show graphs for these samples"to go to a second screen that displays the graphs and key statistics of the samples for each of the eight parameters by selection on the top of the screen. Next, select 2D histograms"to plot combinations of any two parameters via the measure on the X axis and measure on the Y axis dropdown menus on the left of the screen. Click Close"to exit and return to the Display Results"screen.

Then, select the export button on the top left of the screen to save detailed numerical data as a csv file to open and further manipulate in a spreadsheet program. Finally, select Close"to exit the Display Results"screen and go back to the home screen. Click Quit"to ensure saving of the database containing the analyzed video sequences.

Certain parameters of swimming, such as wave initiation rate, activity index, brush stroke, and travel speed gradually declined with age even in favorable genetic backgrounds. On the other hand, body wave number, asymmetry, stretch, and curling parameters trended up with age in wild type and aging mutant adults. Although all nematodes start as healthy adults, some rapidly lose their physical fitness, while others maintain vigor for longer periods of time, indicating bad agers have a considerably shorter health span than graceful agers.

Once mastered, analysis of four swimming worms can be acquired in a matter of minutes. Computation takes about six minutes per video, and can be done remotely. It's feasible to process 250 animals per day.

After watching this video, you should have a good understanding of how to acquire videos of swim trials, and process data to obtain evaluation of locomotion in liquid.

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Journal (Neuroscience)

Journal (Neuroscience)

Automated Analysis of C. elegans Swim Behavior Using CeleST Software

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