VUMC Soil Worm Activity Monitor Mohd Fakhrurrazi Mohd Salleh (EE) Suhaili Harun (EE) Amani Rafie (CompE) Saiful Azlan Adanan (BME) February 17, 2005

Requirements Worms & Tray Microscope CCD camera & Processor Computer & Monitor Picolo Capture Card & software Adobe Premiere software Matlab

Solution Requirements Easy to use Easy to modify Fast More accurate measurements

Worm (Caenorhabditis elegans) A free-living nematode, ~1 mm in length, which lives in a temperate soil environment Has the advantage of being a multicellular organism, which is simple enough to be studied in great detail One of the simplest organisms with a nervous system (neurobiology) About 200 sinusoidal movements per minute

Computer Specifications Pentium 4 Processor (3.20GHz) Microsoft Windows XP Professional 1GB SDRAM Dell Quietkey Keyboard & Mouse 128MB ATI Radeon X300 SE Graphic Card 400GB RAID 1 HardDrive 3.5 Floppy Drive Network Card Single Drive CD/DVD Burner

Hardware Configuration

Operational Concept Turn on the Microscope (power supply), Computer, C-Mount Camera Processor, and the Monitor. Fill up 40 MicroLiter of distilled water into one well in the tray Place the tray with worms under the microscope and place a worm from that tray into the water-filled well (in step 1) using a pick

Operational Concept Cont. Open the Picolo-Card software in the computer and record a movie of the worm (until worm dies) from the microscope. Start the image processing by opening MatLab and load the movie file recorded (in step 4) and run the program. You will now obtain graphical results [[ Pixel speed, total pixel movement, velocity, absolute difference of frames, and area covered ]] Repeat steps 2-6 for a different worm.

Image Processing Analysis Acquire frames from video for few seconds Analysis: Velocity of the worm Area Take the difference of the pixel values between the first two frames (noise elimination) Determine coordinate of centroid Take another difference for the next second frames Determine coordinate of the next centroid and compare to get the displacement Divide with time to acquire its velocity

Example of an image

Segmented image segmented original

Acquire Two Frames Frame 1 Frame 2

|Frame 1 – Frame 2| Frame 1 Frame 2

Determine the centroid Calculated centroid (146,147) Expected centroid

Determine the centroid Calculated centroid (146,147) New calculated centroid (173,155) y Expected centroid x

Determine the centroid Calculated centroid (173,155) – filtered once New calculated centroid (203,172) – filtered twice y Expected centroid x

Determine the centroid New calculated centroid (203,172) – filtered twice Expected centroid = new calculated centroid (202,173) y x

Determine the velocity For worm 1: Average velocity = 23.0954 pps Area = 949 pixels

Determine the velocity For worm 2: Average velocity = 28.045 pps Area = 1181 pixels

Determine the velocity For worm 2: Average velocity = 15.30 pps Area = 583 pixels

Comparison of the worms Observation Fast Very Slow Average Velocity (pps) 23.0954 28.045 15.30 Area (pixels) 949 1181 583 Conclusion Second fastest worm Fastest worm Slow worm

Future Work Ordering the adapter from MEIJI Software development Capturing images of the worm Hardware setup