How to make a bacteria edge tracking?

[Ironmario13]

Hi everyone.

My system has 3 elements

Camera

Microscope

Moving robot with bacteria sample

The objetive is to take a image every 5 seconds (with this VI, you can load the video.avi to simulate it).

The image is saving always with the same name, replacing the previous one.

My problem is that i have no idea in how to get the edge of that bacteria, cause the colors are very similar.

Some idea?

I attach the .vi

The AVI file is this:

https://mega.nz/#!p54FzAgT!9NgSCHag8aTPq_UBOyPjcxAjXPisY6JQPHLhaBPcV3A

Photos of the edge that iI have to track:

[drmathewscolbert]

Hello DR Mario.

After having reviewed your .avi files, i've seen you have ended up with the very same problem two of my students have had this year, I hope my explanation helps you:

When these bacteria are spread over a surface, they will imitate any image you shine on them, capturing a bacterial photograph. This is a groundbreaking demonstration the ability to engineer nature to perform a distributed computation in response to the environment, and a striking example of what the future holds in the exciting new field of synthetic biology.

This is one book I recommend to all my students that end up messed with bacteria study and photography: http://www.hup.harvard.edu/catalog.php?isbn=9780674975910

Regarding the problem of your bacteria's edge and the possibility for it to be photographed i will explain you, with details, what would I do, supposing that you have used once labview or similar software to engage your project. 

Taking photos with a microscope is a hard thing to do: I describe it, after 39 years, as a simple, economical, and highly practical technique for taking digital photographs of specimens visualized through a light microscope. Most models of light microscope and compact digital camera, and even some cameraphones, can be used. The technique is quick to learn and can easily be performed in a resource-poor setting. It can be used to assist with diagnosis in remote areas and can be extremely useful for teaching.

In here I attach you photographs taken by me using this technique, 

Dividing forms of T. brucei (A) and ring form of P. falciparum (B) in peripheral blood film, ×1000 magnification. Corticated A. lumbricoides ovum (C) and T. trichiura ovum (D) in stool, ×400 magnificationThe minimum equipment required for this technique is a microscope with eyepiece and a compact digital camera or cameraphone with auto focus, through-the-lens light meter, minimum ×3 optical zoom, and LCD screen and a microscope with eyepiece and Labview software. The technique is as follows:

• Using the microscope, examine the specimen by eye and select the area of interest and magnification required.
• Increase the light source to maximum intensity.
• Hold the camera lens against the microscope eyepiece. I highly recommend you acquire one of these, they are cheap and super useful, A rubber cup over the eyepiece helps to hold the camera steady. A small circle of light will be seen on the camera's LCD screen.
• Use the camera's zoom function to increase the size of the circle as required. The most difficult step is moving the camera lens small distances across the eyepiece to center the circle. The camera's autofocus should then self-adjust to give a clear image.
• Adjust the fine focus of the microscope to maximise image clarity.
• If the image is too dark or grainy, the camera's ISO setting should be increased (usually 100 or 200 will suffice) or the “darkness” or “night time” setting selected, depending on the model of camera. Note that generally, the higher the ISO, the more difficult it is to obtain a clear image.
• While holding the camera very still, a photograph can be taken, and the image can be examined to see if it is satisfactory. Excessive blur from camera shake can be minimized using a remote control, by attaching the camera to the microscope using sticky tape or bungee cords or by constructing a frame to hold the camera in place.

Obtaining images of clinical specimens viewed by a microscope can be invaluable for both diagnosis and teaching.

Photography by a microscope normally requires a specially adapted microscope with a camera port, a camera with removable lens system, and an adapter to attach the camera to the port.

This equipment is prohibitively expensive for many laboratories, especially in the developing world. The advent of affordable compact digital cameras with displays that reflect precisely the image as seen through the camera lens has made possible a simplified method of taking photographs through a microscope. Almost any combination of light microscope and compact digital camera with optical zoom (including some camera phones) can be used without the need for specialized equipment. Images obtained can be transmitted instantaneously by e-mail or mobile phone picture message for further timely examination by a specialist at another location (e.g., to check species identification of a parasite).

This technique therefore has great potential to enhance clinical care in resource poor settings, including in remote areas. It also enables the accumulation of a library of locally relevant clinical images for use in teaching laboratory staff and clinicians and for documentation in research.

I hope this information has been useful DR Mario, I hope you can succeed in your project and don't hesitate contacting me for further help in case you need it. 

Warmest regards,

DR Mathews