gearing up for research - week 6 & 7
Sunday, July 13, 2008
30 May 2008 & 6 June 2008
Micro PIV: Dynamic Studio Software Training
What have we learnt?
- Some basics on micro fluidics
- How we set the equipment up
- How to operate the equipment and find out the relevant data collected using the software Dynamic Studio
Some Basics on micro fluidics
What have we learnt?
- Some basics on micro fluidics
- How we set the equipment up
- How to operate the equipment and find out the relevant data collected using the software Dynamic Studio
Some Basics on micro fluidics
As what we have learnt in Fluid mechanics, the way fluid flow in a pipe and fluid flow in a micro channel can be totally different.
Micro fluidics is the study of liquid movement in a micro channel using small particles. By using these small particles mixed with the liquid, we are able to monitor the liquid movement with the help of a light source and a camera. When the camera captures a set of images within a period of time, a software will then tabulate the movement of the particles, showing the speed and direction at which is going by using a highly profound statistics.
Equipment set-up
Micro fluidics is the study of liquid movement in a micro channel using small particles. By using these small particles mixed with the liquid, we are able to monitor the liquid movement with the help of a light source and a camera. When the camera captures a set of images within a period of time, a software will then tabulate the movement of the particles, showing the speed and direction at which is going by using a highly profound statistics.
Equipment set-up
Side view on how the syringes is supposed to be positioned
This is the front view on how the chip is positioned onto the microscope
Operating the equipment
After the software is run, Mr Edward taught us how to adjust the time between pulses which are the time difference between two consecutive pulses. The time between pulses depend on the particle velocity. The higher the velocity, the shorter the pulse time we have to set. For example, we chose a pulse time of 100чs. Also, we are able to change the trigger rate which is the frequency of the images that can be taken. For our case, we chose 8Hz as this is according to the requirement of the camera which operate at 10Hz maximum. This means that 8 images are taken per second. Moreover, the number of images to be taken can also be changed. As a trial, we picked 10 images and we chose double frame which means that there are 20 images (10 pairs). Each pair of images are obtained as Frame 1 and Frame 2. We can select whether we want the images taken to be single frame, double frame or single frame with double exposure.
Before everything, we have to open the database that we want then we go to the acquisition mode in which all these options can be done. This can be done by clicking the green icon at the top. Then, we can choose whether to carry out free run, preview, acquire or stop. Basically, the free run allows the software to run continuously with the camera capturing images at selected time interval.
Prior to acquiring the images, we used the microscope to focus on the micro slide. However, the focus on the microscope from the eyepiece and from the camera is different. Hence, we have to adjust the focus based on the camera focus which is shown on the computer. This can be done by turning the focus knob (both fine and coarse) at the microscope. Before we are able to adjust the focus according to the image taken by the camera, we must run the program at preview mode to get the precise image when the LED light and camera is running at the specific timing we adjusted to just that it is not saving any images to the buffer space* or the hard disk of the PC. From what Mr Edward told us, the higher the modifications we made using the microscope focus by choosing a larger objective lens, the smaller will be the depth of field. The depth of field refers to the distance of focus on the object from the objective lens.
*the buffer space is an amount of memory being set aside making use of the RAM of the PC to save images during the run temporarily.
1) After focusing, we must change to single frame mode and acquire. The reason this is being done is to do calibration of the width of the channel so as to obtain the vector, the speed at which the solid particles are moving. After we acquire, we switch the window to acquire data to save the image under calibration. Exit acquisition mode. Under the database that the image is saved in, select the image under calibration.
2) Open the image and right click on the image. Select measure scale factor.
3) In the new window that is opened, click on absolute distance and type 1mm (since the distance between opposite walls in the straight channel is 1mm).
4) Then, select X-Y markers below. Using the instructions given, mark points A and B on the image which represents the respective points on opposite walls.
5) Once done, the scale factor will be shown on the right hand side. Calibration is complete.
In order to start acquiring images, we selected “acquire” button on the right. Once the run is over, the images can be browsed on the acquired data windows. Then, we must save the images unless the images from the 2 frames do not show any difference or dissatisfaction of images captured. If we do not save the images, the software is unable to analyze the pictures as it is not saved into the hard disk of the computer. After we save the images, it is better to clear the buffer images as it will take up unnecessary space on the RAM which may not be enough for subsequent runs.
Furthermore, we can analyse the saved images using various calibration methods such as “Cross-calibration”, “Moving Average calibration” or etc. For our project, Mr Edward informs us that “Cross calibration” is to be used. Hence, by selecting cross calibration, all the saved images are analysed and a new analyzed windows of all the images are opened. These windows show the vectors profile indicated by arrows.
Problems encountered
During our training, we faced a problem with the software. At one point, while Mr Edward was demonstrating the acquisition on the software, the time between pulses kept on changing when we tried to set a certain value. However, after a while, Mr Edward figured the problem and he found out that the camera settings are affecting the time between pulses. This was because the time between pulses has to be set within the camera exposure time.
During our actual day when Mr Edward was not there, we also encountered two problems. While we were setting up the micro slide and introducing the fluid into the syringes, there were many air bubbles formed and trapped inside the tubes and micro channel. To solve this problem, we consulted Mr Edward and he told us to fill the fluid from the big syringe connected to one end of the channel and allow the fluid to flow to the two smaller syringes connected to the other two ends of the channel. By doing this, the air bubbles are removed and we were glad we can continue with our experiment.
Another problem we encountered was that after we acquired the images in the software, we noticed that frame 2 was in complete darkness while frame 1 was well-lit. After a while of finding the cause of the problem, we finally realised that the second pulse width did not coincide with the camera exposure time. As a result, frame two was not exposed to any light resulting in darkness.
Conclusion
In conclusion, we have learnt a few important lessons. These include a basic understanding of fluid flow in micro channel, how to use the Dynamic Studio software and also how to set up the equipment and apparatus for our experiment. Firstly, a basic understanding of micro-fluidic flow gave us a rough idea of how the flow in micro-channel differs from flow in macro-channel such as flow pattern etc. Also, it relates to how the software can be used to determine particle velocity in micro-channel.
Moreover, although learning how to use the software is almost as similar as learning another photo-editing program, the important steps are to be able to precisely select the timing between pulses, camera exposure time as well as analyzing the captured images using the correct correlations and analysis.
Lastly, we learnt how to set up our equipment and apparatus for the experiment. It was a minor attribute but after a few runs on the software, we found out that even the slightest change in set up could result in vast differences in results. Hence, setting up the equipment which includes the syringes and microscope focus correctly definitely affects the results and if not done properly, could end up in long delays.
Before everything, we have to open the database that we want then we go to the acquisition mode in which all these options can be done. This can be done by clicking the green icon at the top. Then, we can choose whether to carry out free run, preview, acquire or stop. Basically, the free run allows the software to run continuously with the camera capturing images at selected time interval.
Prior to acquiring the images, we used the microscope to focus on the micro slide. However, the focus on the microscope from the eyepiece and from the camera is different. Hence, we have to adjust the focus based on the camera focus which is shown on the computer. This can be done by turning the focus knob (both fine and coarse) at the microscope. Before we are able to adjust the focus according to the image taken by the camera, we must run the program at preview mode to get the precise image when the LED light and camera is running at the specific timing we adjusted to just that it is not saving any images to the buffer space* or the hard disk of the PC. From what Mr Edward told us, the higher the modifications we made using the microscope focus by choosing a larger objective lens, the smaller will be the depth of field. The depth of field refers to the distance of focus on the object from the objective lens.
*the buffer space is an amount of memory being set aside making use of the RAM of the PC to save images during the run temporarily.
1) After focusing, we must change to single frame mode and acquire. The reason this is being done is to do calibration of the width of the channel so as to obtain the vector, the speed at which the solid particles are moving. After we acquire, we switch the window to acquire data to save the image under calibration. Exit acquisition mode. Under the database that the image is saved in, select the image under calibration.
2) Open the image and right click on the image. Select measure scale factor.
3) In the new window that is opened, click on absolute distance and type 1mm (since the distance between opposite walls in the straight channel is 1mm).
4) Then, select X-Y markers below. Using the instructions given, mark points A and B on the image which represents the respective points on opposite walls.
5) Once done, the scale factor will be shown on the right hand side. Calibration is complete.
In order to start acquiring images, we selected “acquire” button on the right. Once the run is over, the images can be browsed on the acquired data windows. Then, we must save the images unless the images from the 2 frames do not show any difference or dissatisfaction of images captured. If we do not save the images, the software is unable to analyze the pictures as it is not saved into the hard disk of the computer. After we save the images, it is better to clear the buffer images as it will take up unnecessary space on the RAM which may not be enough for subsequent runs.
Furthermore, we can analyse the saved images using various calibration methods such as “Cross-calibration”, “Moving Average calibration” or etc. For our project, Mr Edward informs us that “Cross calibration” is to be used. Hence, by selecting cross calibration, all the saved images are analysed and a new analyzed windows of all the images are opened. These windows show the vectors profile indicated by arrows.
Problems encountered
During our training, we faced a problem with the software. At one point, while Mr Edward was demonstrating the acquisition on the software, the time between pulses kept on changing when we tried to set a certain value. However, after a while, Mr Edward figured the problem and he found out that the camera settings are affecting the time between pulses. This was because the time between pulses has to be set within the camera exposure time.
During our actual day when Mr Edward was not there, we also encountered two problems. While we were setting up the micro slide and introducing the fluid into the syringes, there were many air bubbles formed and trapped inside the tubes and micro channel. To solve this problem, we consulted Mr Edward and he told us to fill the fluid from the big syringe connected to one end of the channel and allow the fluid to flow to the two smaller syringes connected to the other two ends of the channel. By doing this, the air bubbles are removed and we were glad we can continue with our experiment.
Another problem we encountered was that after we acquired the images in the software, we noticed that frame 2 was in complete darkness while frame 1 was well-lit. After a while of finding the cause of the problem, we finally realised that the second pulse width did not coincide with the camera exposure time. As a result, frame two was not exposed to any light resulting in darkness.
Conclusion
In conclusion, we have learnt a few important lessons. These include a basic understanding of fluid flow in micro channel, how to use the Dynamic Studio software and also how to set up the equipment and apparatus for our experiment. Firstly, a basic understanding of micro-fluidic flow gave us a rough idea of how the flow in micro-channel differs from flow in macro-channel such as flow pattern etc. Also, it relates to how the software can be used to determine particle velocity in micro-channel.
Moreover, although learning how to use the software is almost as similar as learning another photo-editing program, the important steps are to be able to precisely select the timing between pulses, camera exposure time as well as analyzing the captured images using the correct correlations and analysis.
Lastly, we learnt how to set up our equipment and apparatus for the experiment. It was a minor attribute but after a few runs on the software, we found out that even the slightest change in set up could result in vast differences in results. Hence, setting up the equipment which includes the syringes and microscope focus correctly definitely affects the results and if not done properly, could end up in long delays.
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