Recording Live Videos from a Microscope

Recording live videos from a microscope offers some advantages over taking the snapshot pictures.  This is especially true when you are observing the live organisms.  You are not only recording the images at specific time but also the sequences of images continuously.  Moving cilia and locomotion of Diatom can be captured by live video but not the snapshot picture.  You can records the organisms changes their shapes or images from different angles where you have to take many shots with snapshot pictures.  Sometimes it is easier to identify the organisms with videos rather than using snapshot pictures.  You can identify them not only with their morphology but also their behavior.  Most of all, watching videos are fun, it give you the sense of live.  Most digital cameras made today equipped with video capturing capability, it makes video capturing much easier.  If you are already using a digital camera (either a consumer digital camera or specialized microscope camera) for taking pictures, most likely you are ready to take live videos. 

A rotifer recorded at 400x.  The movement of the cilia is clearly visible.  The video was shrinked to smaller size due to wordpress, clicking on the video to see it in youtube.com.

You can take videos using snapshot cameras, DSLRs or camcorders, specialized microscope cameras offers some advantages over these other options.  It is easier to focus with computer screens rather than small viewfinders.  The microscope camera also provides the remote capturing capability and the convenience of saving the videos on computer’s hard drives (your microscope camera might already mounted on the trinocular port).  The disadvantage is that they are completely relying on computer software and limited by the computer hardware.  The focus of this page is to discuss the factors affecting the quality of live video and to provide you some tips for better videos with a microscope camera.  

Computer Hardware Recording the videos with microscope is like taking sequences of images (called frames), transferred through the data cable, processed through the video capturing software and stored in the hard drive.  It requires significant computing power to perform those tasks simultaneously.  Video files are significant larger than the snapshot pictures.   The video capturing software also require significant amount of memory for image processing.  Today, CPUs are getting faster and the memory and hard drives are getting bigger.  Recoding high quality videos with higher resolution and frame rates are easier.  To recording a live HD* videos, I’d like to recommend you to have at least a computer with a dual core processor, minimum of 3 GB of memory and as much hard drive space as possible.  This is very entry computer configuration at the time of the writing.

Video Capturing Software Most microscope cameras completely rely on computer software to perform image processing, such as white balance, auto exposure, contrast, brightness etc…  These settings directly affect the image quality so are the video captured by the software.  Video compression also affects the image quality.  Uncompressed videos are excessively large.  Considering taking a video at 1 MP at 25 frames per second for 40 seconds, it will be take up 1GB hard drive space.  They are unsuitable for distribution and sharing.  Fortunately, you can use video compression to make the video files much smaller – at the expenses of some CPU power. 

I recorded this vorticella video in HD resolution at 1024 x 768 (converted to 720p when uploaded to youtube) at 8 fps with xVid compression using Tucsen microscope camera and TSVeiw software.  It runs about 2 minutes and 30 seconds, while merely took 5MP in size.  It will easily take up to a couple GB if not compressed.  The video sacrifice the frame rate for the recording length and resolution with a slice of CPU processing power allocated to video compression.  The frame rate would have been 16 fps if not compressed.

How video capturing software saves the video files also affects the video quality.  Some Video software, like MICAM, stores the video temporarily in memory while steaming the video and save it to hard drive after the recording.  It provides higher frame rate, however, the recording time is limitted by the amount of memory.  A short 12 second uncompressed video at 1024x 768 can easily takes 1GB of memory.  Some video software, like TSView, stores the video file in hard drive when streaming the video through the USB cable.   The advantage of this mode is able to record long video however, the frame rate is significantly lower.  I was able to record videos with MICAM in 25 frame per second (fps) but it is only limitted to 16 fps by TSView.  However, the video length is limitted to 12 seconds due to the amount of memory of my laptop with MICAM.

Resolution, Frame Rate and Video Length These are, in fact, the indicators of the quality of a video.  Different from microscope resolution, the resolution of a video is the height and width of a video expressed as number of pixels.  The higher the resolution the larger the video when they are displayed on the same screen.  The higher the frame rate the better the quality is.  With higher frame rate, you can see continuous movement without choppy motion or skipping frames.  However, resolution and frame rate has inversely related.  The frame is dropped significantly as you increase the resolution.   It is desirable to record longer videos.  However, the video files will be enormous if it is not compressed.  Sometime it is desirable to reduce resolution or frame rate to exchange for longer recording length.

Tips for recording good videos

• Bigger is not necessary better: For fast moving critters, it might be more desirable for faster frame rate.  You might want to sacrifice the resolution for faster frame rate by recording 640 x 480 rather than full HD resolution.
• Slow your organism down:  Sometime it is impossible to capture your organism is full speed.  You might want to slow them down with thickening agents or narcotics.
• Defragment the hard drive and close unneeded application: The quality of the video directly related to the capability of your computer.  If you are using the software like TSView, the recording frame rate can be limited by the hard drive speed.  If you have not defragment your hard drive for a long time, it might become slow.  Defragment the hard drive will help.  Close down some program or disable anti-virus software can also free up some computing resources for your video capturing software.
• Setting correct exposure: Enable for you to achieve higher frame rate, you have to reduce exposure time.  You can do this by turning off the auto exposure and adjust the exposure time manually.  Turning up the light intensity will compensate the loss of light due to shorter exposure time.

You may not need the same frame rate for recording the amoeba locomotion and the rotifer cilia movement or the zipping Cyclidium.

• Experiment with different video compression settings: Try to experiment with different compression and quality settings.  Some video compression algorithms are more CPU intensive than others.  When you use higher quality settings, you will end up with smaller file, and vice versa.
• Lots of practice for the correct setting: Just like any things, adjust manual setting for your camera needs some experiences.  Practice will help.
• Use the right objective lens: Depending on what you want to observe, you might want to use lower power lens so you can record their movement.  It is annoying for the view to see you keep moving the mechanical stage trying to track the moving organism.  Lower power lens also give you more light which is essential for faster frame rate.

At 100x, the locomotion of rotifer is easily captured.  Rotifers sometime crawl like an inch worm. They use the adhesive gland on both end of their body and stretch their body to move. Sometime they swim like submarines. They move the ciliates on trochus in helical motion to propel forward. 

• Make sure that you have the right computer hardware*: Recording video is a CPU and memory intensive process.   You want to make sure that it has the spec to handle the task.  You might want to upgrade the memory if it is less than 2 GB.  An entry level computer today will be good enough for recording HD video.  If your computer is more than five years old, it might be the time to replace it anyway.

* For reference purpose: I used my HP pavilion dv2700 laptop for video recording.  The laptop uses Intel duo core processor T5500 @1.83 GHz with 3GB of memory and 230GB hard drive running on Windows Vista Home Premium operating system.  This laptop has many other programs installed aside from the factory installed programs so the performance is not optimum.

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