Confocal Microscopy - Revision history

Wang Tingyu1976: /* Matlab Code */

2022-05-07T02:26:11Z

Matlab Code

← Older revision		Revision as of 02:26, 7 May 2022
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	====Matlab Code====		====Matlab Code====
	This SerialCom_Read.m program will build up serial communication between MATLAB and Arduino Board. The Arduino Board will read data from Photodiode and send data to MATLAB with a baud rate of 115200 (maximum of 115200 bits per second).		This SerialCom_Read.m program will build up serial communication between MATLAB and Arduino Board. The Arduino Board will read data from Photodiode and send data to MATLAB with a baud rate of 115200 (maximum of 115200 bits per second).
	[[File:Fig n.png\|~~x800px~~\|center\|thumb]]		[[File:Fig n.png\|x750px\|center\|thumb]]
	This program will process data and calculate the Height and Intensity Matrix		This program will process data and calculate the Height and Intensity Matrix
	[[File:Fig_h.png\|x800px\|center\|thumb]]		[[File:Fig_h.png\|x800px\|center\|thumb]]

Wang Tingyu1976: /* Matlab Code */

2022-05-07T02:25:42Z

Matlab Code

← Older revision		Revision as of 02:25, 7 May 2022
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	====Matlab Code====		====Matlab Code====
	This SerialCom_Read.m program will build up serial communication between MATLAB and Arduino Board. The Arduino Board will read data from Photodiode and send data to MATLAB with a baud rate of 115200 (maximum of 115200 bits per second).		This SerialCom_Read.m program will build up serial communication between MATLAB and Arduino Board. The Arduino Board will read data from Photodiode and send data to MATLAB with a baud rate of 115200 (maximum of 115200 bits per second).
	[[File:~~Fig_n~~.png\|x800px\|center\|thumb]]		[[File:Fig n.png\|x800px\|center\|thumb]]
	This program will process data and calculate the Height and Intensity Matrix		This program will process data and calculate the Height and Intensity Matrix
	[[File:Fig_h.png\|x800px\|center\|thumb]]		[[File:Fig_h.png\|x800px\|center\|thumb]]

XUE RUI: /* Remained Problems and Future Works */

2022-05-07T02:24:11Z

Remained Problems and Future Works

← Older revision		Revision as of 02:24, 7 May 2022
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	The last problem is that our system can't achieve quite accurate height information about the scanned area, so 3D profiling remains a problem. Some factors might be responsible for the inaccurate height information in the coin scanning. For instance, we did a 1mm1mm scan with a resolution of only 1010, which is quite low to depict more detailed surface information, however, higher resolution means more time consuming. Another possible factor is the imperfection in our data processing program, this might cause us found a wrong maximum point and thus gave us a wrong height of the focused point.		The last problem is that our system can't achieve quite accurate height information about the scanned area, so 3D profiling remains a problem. Some factors might be responsible for the inaccurate height information in the coin scanning. For instance, we did a 1mm1mm scan with a resolution of only 1010, which is quite low to depict more detailed surface information, however, higher resolution means more time consuming. Another possible factor is the imperfection in our data processing program, this might cause us found a wrong maximum point and thus gave us a wrong height of the focused point.

	Except solving those problems mentioned above and increase the efficiency and precision of our confocal microscopy, there are still some functions we wish to achieve on our Laser Scanning Setup. ~~First is that we~~ wish to achieving the detection of fluorescence other than reflected light, we will need an optical filter to filter out the reflected light and a much more sensitive sensor to detect and collect the fluorescence light. Longer scanning time each point might be able to offset the requirement on sensor, yet this will also decrease the efficiency of the scanning system. With the fluorescence detection ability, we will try to detect some living creatures based on this system.		Except solving those problems mentioned above and increase the efficiency and precision of our confocal microscopy, there are still some functions we wish to achieve on our Laser Scanning Setup. We wish to achieving the detection of fluorescence other than reflected light, we will need an optical filter to filter out the reflected light and a much more sensitive sensor to detect and collect the fluorescence light. Longer scanning time each point might be able to offset the requirement on sensor, yet this will also decrease the efficiency of the scanning system. With the fluorescence detection ability, we will try to detect some living creatures based on this system.

	==Lab Location==		==Lab Location==

	S12-01-10/11 Nanomaterials Research Lab		S12-01-10/11 Nanomaterials Research Lab

Wang Tingyu1976: /* Discussion */

2022-05-07T02:23:00Z

Discussion

@@ Line 104: / Line 104: @@
 The final 3D results are shown in Figure 12. From that, it can be find that we have realised the three-dimensional imaging by confocal microscope.
 [[File:Fig g.png|x350px|center|thumb|Figure 12. 3D results of DrawTopo.m]]
 ==Discussion==

Wang Tingyu1976: /* Data Processing */

2022-05-07T02:22:44Z

Data Processing

@@ Line 74: / Line 74: @@
 ====Step 3====
 At last, we moved 100um on x-axis through tuning the spiral and measured the final set of data.
 =Experimental results=

XUE RUI: /* Matlab Code */

2022-05-07T02:13:49Z

Matlab Code

← Older revision		Revision as of 02:13, 7 May 2022
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	===Data Processing===		===Data Processing===
	====Matlab Code====		====Matlab Code====
	This		This SerialCom_Read.m program will build up serial communication between MATLAB and Arduino Board. The Arduino Board will read data from Photodiode and send data to MATLAB with a baud rate of 115200 (maximum of 115200 bits per second).

			This program will process data and calculate the Height and Intensity Matrix
	[[File:Fig_h.png\|x800px\|center\|thumb]]		[[File:Fig_h.png\|x800px\|center\|thumb]]
	~~This~~
	[[File:Fig i.png\|x820px\|center\|thumb]]		[[File:Fig i.png\|x820px\|center\|thumb]]
	~~This~~
	[[File:Fig_j.png\|x220px\|center\|thumb]]		[[File:Fig_j.png\|x220px\|center\|thumb]]
	This		This program will filter out Noise and calculate AC, BC
	[[File:Fig k.png\|x700px\|center\|thumb]]		[[File:Fig k.png\|x700px\|center\|thumb]]
	This		This program will draw 2D image of the scanned area
	[[File:Fig_l.png\|x140px\|center\|thumb]]		[[File:Fig_l.png\|x140px\|center\|thumb]]
	This		This program will draw 3D profile of the scanned sample area
	[[File:Fig m.png\|x650px\|center\|thumb]]		[[File:Fig m.png\|x650px\|center\|thumb]]

XUE RUI: /* Matlab Code */

2022-05-07T02:03:57Z

Matlab Code

← Older revision		Revision as of 02:03, 7 May 2022
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	This		This
	[[File:Fig_h.png\|x800px\|center\|thumb]]		[[File:Fig_h.png\|x800px\|center\|thumb]]
			This
	[[File:Fig i.png\|x820px\|center\|thumb]]		[[File:Fig i.png\|x820px\|center\|thumb]]
			This
	[[File:Fig_j.png\|x220px\|center\|thumb]]		[[File:Fig_j.png\|x220px\|center\|thumb]]
			This
	[[File:Fig k.png\|x700px\|center\|thumb]]		[[File:Fig k.png\|x700px\|center\|thumb]]
			This
	[[File:Fig_l.png\|x140px\|center\|thumb]]		[[File:Fig_l.png\|x140px\|center\|thumb]]
			This
	[[File:Fig m.png\|x650px\|center\|thumb]]		[[File:Fig m.png\|x650px\|center\|thumb]]

XUE RUI: /* Matlab Code */

2022-05-07T02:03:26Z

Matlab Code

← Older revision		Revision as of 02:03, 7 May 2022
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	===Data Processing===		===Data Processing===
	====Matlab Code====		====Matlab Code====
			This
	[[File:Fig_h.png\|x800px\|center\|thumb]]		[[File:Fig_h.png\|x800px\|center\|thumb]]
	[[File:Fig i.png\|x820px\|center\|thumb]]		[[File:Fig i.png\|x820px\|center\|thumb]]

XUE RUI: /* Experimental results */

2022-05-06T07:38:12Z

Experimental results

← Older revision		Revision as of 07:38, 6 May 2022
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	We used two piezo stage to move along y and z axis automatically, and a spiral micrometer to move the stage along x axis. Here we want to scan 10 points along x axis, 10 points along y axis and 80 points along z axis. Here is how we scan our sample: start from (x,y,z) the receiver will automatically scan 80 points when piezo moves upward along z axis (for scanning of each point piezo will take for about 85ms) and reach point (x,y,z+400), it will go pass the focused point of this certain (x,y) along the scanning of z axis, then piezo will move to point (x,y+100,z+400) and hold there for 5 seconds, then it will movie downward and reach point (x,y+100,z), it will pass through the focused point of this (x,y+400), and after that, it will move to point (x,y+200,z) and hold there still for 5 seconds. After 5 iterations of this, we will reach point (x,y+1000,z) and then we will use micrometer move the stage manually to point (x+100, y+1000,z) and repeat another 5 iterations, after moving 9 times we will reach point (x+1000, y+1000,z) finally. Figure ~~below~~ is the typical scanning pattern of two points (x,y,z+400) and (x,y+100,z+400), so we can find two corresponding maximum A&B in the plot, C is the point when piezo starts to hold still for 5 seconds.		We used two piezo stage to move along y and z axis automatically, and a spiral micrometer to move the stage along x axis. Here we want to scan 10 points along x axis, 10 points along y axis and 80 points along z axis. Here is how we scan our sample: start from (x,y,z) the receiver will automatically scan 80 points when piezo moves upward along z axis (for scanning of each point piezo will take for about 85ms) and reach point (x,y,z+400), it will go pass the focused point of this certain (x,y) along the scanning of z axis, then piezo will move to point (x,y+100,z+400) and hold there for 5 seconds, then it will movie downward and reach point (x,y+100,z), it will pass through the focused point of this (x,y+400), and after that, it will move to point (x,y+200,z) and hold there still for 5 seconds. After 5 iterations of this, we will reach point (x,y+1000,z) and then we will use micrometer move the stage manually to point (x+100, y+1000,z) and repeat another 5 iterations, after moving 9 times we will reach point (x+1000, y+1000,z) finally. Figure 9 is the typical scanning pattern of two points (x,y,z+400) and (x,y+100,z+400), so we can find two corresponding maximum A&B in the plot, C is the point when piezo starts to hold still for 5 seconds.

	By getting length AC and BC, we can calculate height and intensity information about each (x, y). I use MATLAB function NF.m to filter noise and Figure.9 illustrates the filtered data. Here is how we convert AC and BC to height Information. AC and BC are actually number of data points (in the spacing). We know that Arduino will sent one data to MATLAB every 25ms, so AC and BC can be converted to time. Then we know that the scanning speed of piezo stage along z axis is about 59um/s (micrometer per second), hence AC and BC can be converted to distance. Here AC and BC indicates the distance of two maximum (focused) points to the upper surface, using total height 400um to subtract AC ~~and~~ BC will give us the height of ~~these two maximum points~~ (to the lower surface).		By getting length AC and BC, we can calculate height and intensity information about each (x, y). I use MATLAB function NF.m to filter noise and Figure.9 illustrates the filtered data. Here is how we convert AC and BC to height Information. AC and BC are actually number of data points (in the spacing). We know that Arduino will sent one data to MATLAB every 25ms, so AC and BC can be converted to time. Then we know that the scanning speed of piezo stage along z axis is about 59um/s (micrometer per second), hence AC and BC can be converted to distance. Here AC and BC indicates the distance of two maximum (focused) points A and B to the upper surface, using total height 400um to subtract AC, BC will give us the height of A,B (to the lower surface).

	[[File:Fig b.png\|x400px\|center\|thumb\|Figure 9. Typical scanning pattern of two points (x,y,z+400) and (x,y+100,z+400)]]		[[File:Fig b.png\|x400px\|center\|thumb\|Figure 9. Typical scanning pattern of two points (x,y,z+400) and (x,y+100,z+400)]]

XUE RUI: /* Experimental results */

2022-05-06T07:34:47Z

Experimental results

← Older revision		Revision as of 07:34, 6 May 2022
Line 92:		Line 92:
	We used two piezo stage to move along y and z axis automatically, and a spiral micrometer to move the stage along x axis. Here we want to scan 10 points along x axis, 10 points along y axis and 80 points along z axis. Here is how we scan our sample: start from (x,y,z) the receiver will automatically scan 80 points when piezo moves upward along z axis (for scanning of each point piezo will take for about 85ms) and reach point (x,y,z+400), it will go pass the focused point of this certain (x,y) along the scanning of z axis, then piezo will move to point (x,y+100,z+400) and hold there for 5 seconds, then it will movie downward and reach point (x,y+100,z), it will pass through the focused point of this (x,y+400), and after that, it will move to point (x,y+200,z) and hold there still for 5 seconds. After 5 iterations of this, we will reach point (x,y+1000,z) and then we will use micrometer move the stage manually to point (x+100, y+1000,z) and repeat another 5 iterations, after moving 9 times we will reach point (x+1000, y+1000,z) finally. Figure below is the typical scanning pattern of two points (x,y,z+400) and (x,y+100,z+400), so we can find two corresponding maximum A&B in the plot, C is the point when piezo starts to hold still for 5 seconds.		We used two piezo stage to move along y and z axis automatically, and a spiral micrometer to move the stage along x axis. Here we want to scan 10 points along x axis, 10 points along y axis and 80 points along z axis. Here is how we scan our sample: start from (x,y,z) the receiver will automatically scan 80 points when piezo moves upward along z axis (for scanning of each point piezo will take for about 85ms) and reach point (x,y,z+400), it will go pass the focused point of this certain (x,y) along the scanning of z axis, then piezo will move to point (x,y+100,z+400) and hold there for 5 seconds, then it will movie downward and reach point (x,y+100,z), it will pass through the focused point of this (x,y+400), and after that, it will move to point (x,y+200,z) and hold there still for 5 seconds. After 5 iterations of this, we will reach point (x,y+1000,z) and then we will use micrometer move the stage manually to point (x+100, y+1000,z) and repeat another 5 iterations, after moving 9 times we will reach point (x+1000, y+1000,z) finally. Figure below is the typical scanning pattern of two points (x,y,z+400) and (x,y+100,z+400), so we can find two corresponding maximum A&B in the plot, C is the point when piezo starts to hold still for 5 seconds.

	By ~~calculating~~ length AC and BC, we can ~~get~~ height and intensity information about each (x, y). I use MATLAB function NF.m to filter noise and Figure.9 illustrates the filtered data.		By getting length AC and BC, we can calculate height and intensity information about each (x, y). I use MATLAB function NF.m to filter noise and Figure.9 illustrates the filtered data. Here is how we convert AC and BC to height Information. AC and BC are actually number of data points (in the spacing). We know that Arduino will sent one data to MATLAB every 25ms, so AC and BC can be converted to time. Then we know that the scanning speed of piezo stage along z axis is about 59um/s (micrometer per second), hence AC and BC can be converted to distance. Here AC and BC indicates the distance of two maximum (focused) points to the upper surface, using total height 400um to subtract AC and BC will give us the height of these two maximum points (to the lower surface).

	[[File:Fig b.png\|x400px\|center\|thumb\|Figure 9. Typical scanning pattern of two points (x,y,z+400) and (x,y+100,z+400)]]		[[File:Fig b.png\|x400px\|center\|thumb\|Figure 9. Typical scanning pattern of two points (x,y,z+400) and (x,y+100,z+400)]]

← Older revision		Revision as of 02:03, 7 May 2022
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	This		This
	[[File:Fig_h.png\|x800px\|center\|thumb]]		[[File:Fig_h.png\|x800px\|center\|thumb]]
			This
	[[File:Fig i.png\|x820px\|center\|thumb]]		[[File:Fig i.png\|x820px\|center\|thumb]]
			This
	[[File:Fig_j.png\|x220px\|center\|thumb]]		[[File:Fig_j.png\|x220px\|center\|thumb]]
			This
	[[File:Fig k.png\|x700px\|center\|thumb]]		[[File:Fig k.png\|x700px\|center\|thumb]]
			This
	[[File:Fig_l.png\|x140px\|center\|thumb]]		[[File:Fig_l.png\|x140px\|center\|thumb]]
			This
	[[File:Fig m.png\|x650px\|center\|thumb]]		[[File:Fig m.png\|x650px\|center\|thumb]]