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resources:eval:user-guides:circuits-from-the-lab:cn0503:fluorescence [02 Aug 2021 19:45]
Angelo Nikko Catapang
resources:eval:user-guides:circuits-from-the-lab:cn0503:fluorescence [21 Jan 2022 21:46]
Angelo Nikko Catapang
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 <note important>​You can use either path 1 or 4 for fluorescence measurements. The steps outlined here will use path 1, and setting LED1, P1ASEL, and P1BSEL.</​note>​ <note important>​You can use either path 1 or 4 for fluorescence measurements. The steps outlined here will use path 1, and setting LED1, P1ASEL, and P1BSEL.</​note>​
-  - Connect the 365nm LED Board and the 615nm LED Board to LED1.\\ {{ :​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_ledplacement.jpg?​nolink&​600 |}} +  - Connect the 365nm LED Board and the 615nm LED Board to LED1.\\ {{:​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_ledplacement.jpg?​nolink&​400|}} 
-  - Place the fluorescent filter into the slot in front of PD1B. and set the jumper connection as below:\\ {{:​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_fluorescentfilter.png?​400 |}}+  - Place the fluorescent filter into the slot in front of PD1B. and set the jumper connection as below:\\ {{:​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_fluorescentfilter.png?​nolink&400 |}}
  
 ^ Jumper Header ​           ^ Setting ​     ^ Image ^ ^ Jumper Header ​           ^ Setting ​     ^ Image ^
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   - Connect the EVAL-ADICUP3029 to the EVAL-CN0503-ARDZ and connect a microUSB-to-USB cable from the board to the host computer.   - Connect the EVAL-ADICUP3029 to the EVAL-CN0503-ARDZ and connect a microUSB-to-USB cable from the board to the host computer.
-  - Run the software (using python scripts or the executable) and wait for the main window to open.\\ {{ :​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​ph_mainwindow.png?​nolink&​600 |}} +  - Run the software (using python scripts or the executable) and wait for the main window to open.\\ {{:​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​ph_mainwindow.png?​nolink&​600|}} 
-  - Click the Gear icon at the top right of the window to open Settings.\\ {{ :​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​ph_opensettings.png?​nolink&​600 |}} +  - Click the Gear icon at the top right of the window to open Settings.\\ {{:​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​ph_opensettings.png?​nolink&​600|}} 
-  - In the settings window, select the correct COM Port of the device and connect (see {{ :​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​cn0503_gui_quick_start_guide.docx | Quick Setup Guide }} for help)\\ {{ :​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​ph_clickconnect.png?​nolink&​600 |}}+  - In the settings window, select the correct COM Port of the device and connect (see {{ :​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​cn0503_gui_quick_start_guide.docx | Quick Setup Guide }} for help)\\ {{:​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​ph_clickconnect.png?​nolink&​600|}}
   - Load the configuration file for Fluorescence Measurement ({{ :​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​cn0503_defaults_fluorescence.zip |}})   - Load the configuration file for Fluorescence Measurement ({{ :​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​cn0503_defaults_fluorescence.zip |}})
-  - Configure the settings for path 1 with the desired name (e.g. Quinine), set wavelength to 365.0, and select measurement type: Fluorescence.\\ {{ :​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_pathsetting.png?​nolink&​600 |}} +  - Configure the settings for path 1 with the desired name (e.g. Quinine), set wavelength to 365.0, and select measurement type: Fluorescence.\\ {{:​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_pathsetting.png?​nolink&​600|}} 
-  - Add empty cuvette/s (or filled with distilled water) to the cuvette holder assembly, and insert to path 1. Set the jumper connection of P1ASEL temporarily to 0DEG. This uses the transmit photodiode directly in the path of light from LED1 to check and measure the intensity of the light source.\\ {{ :​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_optimizeled.jpg?​nolink&​600 |}}+  - Add empty cuvette/s (or filled with distilled water) to the cuvette holder assembly, and insert to path 1. Set the jumper connection of P1ASEL temporarily to 0DEG. This uses the transmit photodiode directly in the path of light from LED1 to check and measure the intensity of the light source.\\ {{:​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_optimizeled.jpg?​nolink&​600|}}
   - Click Optimize LED. This properly sets the LED current in the path so that the light intensity measured by the photodetector is close to 50%.   - Click Optimize LED. This properly sets the LED current in the path so that the light intensity measured by the photodetector is close to 50%.
-  - Return the P1ASEL jumper connection to 90DEG and click Okay here and on the settings window to go back to the main. Remove the empty cuvette or distilled water sample.\\ {{ :​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_returnjumper.jpg?​nolink&​600 |}} +  - Return the P1ASEL jumper connection to 90DEG and click Okay here and on the settings window to go back to the main. Remove the empty cuvette or distilled water sample.\\ {{:​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_returnjumper.jpg?​nolink&​600|}} 
-  - Place a cuvette with filled with tonic water sample levelled just below the marking, as shown below, to the cuvette holder in path 1.\\ {{ :​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_cuvette.jpg?​nolink&​400 |}} +  - Place a cuvette with filled with tonic water sample levelled just below the marking, as shown below, to the cuvette holder in path 1.\\ {{:​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_cuvette.jpg?​nolink&​400|}} 
-  - Select path 1, set display mode to INS1, and press Start Measurement. The concentration of quinine in g/L will be shown in a live plot as shown below.\\ {{ :​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_data.png?​nolink&​600 |}}\\ For quick demo purposes, the system was configured in path 1, by default, ​for the Beer-Lambert conversion of the intensity ratio to quinine concentration as shown in the equation below. Check the [[resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fluorescence#​computing_concentration | Computing Concentration]] section for the mathematical ​details ​on this.\\ {{ :​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_beerlambert.png?​nolink&​600 |}}\\  +  - Select path 1, set display mode to INS1, and press Start Measurement. The concentration of quinine in g/L will be shown in a live plot as shown below.\\ {{:​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_data.png?​nolink&​600|}}\\ For quick demo purposes, the system was configured in path 1, by default, ​using a polynomial approximation. Check the [[resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fluorescence#​computing_concentration | Computing Concentration]] section for more details.\\  
-<note important>​Optionally,​ you can set the unit displayed in the plot to g/L by writing this in the primary unit field of path 1 found by clicking the Advanced button in the Settings window.\\ {{ :​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_advancedunits.png?​nolink&​600 |}}</​note>​+<note important>​Optionally,​ you can set the unit displayed in the plot to g/L by writing this in the primary unit field of path 1 found by clicking the Advanced button in the Settings window.\\ {{:​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fluoresenceunit.png?​nolink&​600|}}</​note>​
  
 ===== Computing Concentration ===== ===== Computing Concentration =====
  
-The CN0503 measures the light intensity of the incident ​light through a reference ​photodiode and the light intensity of the fluorescent ​light through a right angle photodiode. ​This section details ​the mathematical method ​of calculating ​the concentration ​of the target fluorescent material in the solution from raw light intensity 16-bit ADC values ​and the polynomial approximation of the re-arranged Beer-Lambert equation.\\ +The CN0503 measures the intensity of the fluorescent ​light through a right angle photodiode and the intensity of the incident ​light through a reference ​photodiode. ​A polynomial approximation for computing quinine concentration can be modeled using the ratios ​of the two intensities measured from samples ​of known values.\\ ​
 <note important>​The configuration file in ({{ :​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​cn0503_defaults_fluorescence.zip |}}) has already been set up to include everything in this section to calculate the concentration of quinine. There is no need to perform the steps below unless to make changes in the calculation.</​note>​ <note important>​The configuration file in ({{ :​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​cn0503_defaults_fluorescence.zip |}}) has already been set up to include everything in this section to calculate the concentration of quinine. There is no need to perform the steps below unless to make changes in the calculation.</​note>​
-  - The first and most important variable is the ratio of the incident ​light intensity ​to emitted ​light intensity. The CN0503 denotes each sampled light intensity in the format <light path><​photodiode number> ​(e.g. A1 for first light path and the first photodiode). For path 1 and 4, the first photodiode can be either ​the transmit photodiodedirectly in the light pathor the fluorescent photodiode, ​configurable ​through the P1ASEL and P4ASEL, respectively. By default, the CN0503 adds a digital raw adc offset of 2048. Thusthe equation for the ratio can be written as shown in the equation belowThis is defined in the CN0503 application as the absolute ratio ARAT and set using the **DEFX ARAT** command ​also shown below.\\ {{ :​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_arat.png?​nolink&​600 |}} +  - The ratio of the fluorescent ​light intensity ​and incident ​light intensity ​is calculated using the CN0503 firmware and is called the **absolute ratio (ARAT)**. 
-  - The CN0503 allows setting a baseline ratio to remove small factors contributed by the optical glass elements such as the beams splitter, lens, and filters. This can be used if a quinine solution of known concentration is available. For this demo, it will not be used and is set to 1. The result of referencing the obtained ​ARAT to a baseline ratio is defined as the relative ratio RRAT.\\ {{ :​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_rrat.png?​nolink&​600 |}} +  - The computation of the ARAT is configurable through software in reverse polish notation (RPN). The variable naming ​format ​for the measured light intensities is shown below:\\ <​code>​ 
-  - The CN0503 application does not implement a mathematical log operation. Instead, it uses a 5th-order polynomial approximation ​to convert ​the relative ratios ​to desired valuesUsing Microsoft Excel, the quinine concentration ​is calculated ​for several ​data points ​from set values of the relative ratio.\\ {{ :​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_exceldata.png?​nolink&​600 |}} +<light path><​photodiode number> 
-  - The 5th-order polynomial approximation can be obtained from the trendline of the xy scatter plot of the data.\\ {{ :​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_trendline.png?nolink |}}\\ +where:  
 +<light path> = A for path 1, B for path 2, C for path 3, D for path 4 
 +<photodiode ​number> = 1, 2 
 +</​code>​For path 1 and 4, the photodiode ​can be configured to the transmit photodiode ​(directly in the light pathor the right-angle (fluorescentphotodiode, through the P1ASEL and P4ASEL ​headers, respectively, ​while photodiode 2 can be configured to the right-angle (fluorescent) photodiode or the reference (incident) photodiodeYou can use the **DEFX ARAT** command ​to change the ARAT equation. The example ​shown below sets the ARAT computation in path 1 which subtracts a 2048 raw ADC offset from each light intensity value in the ratio.\\ {{:​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_aratcmd.png?​nolink&​400|}} 
 +  - **Optionally**,​ the CN0503 allows setting a baseline ratio to remove small factors contributed by the optical glass elements such as the beams splitter, lens, and filters. The ARAT value is divided by the baseline ratio to produce ​the relative ratio (RRAT). The common way to set the baseline ratio is to take the average ARAT when its expected value is 1For this demo, the baseline ratio is neglected and set to 1 
 +  - Using samples with known quinine concentration, the measured RRAT values ​for each are used as data points ​for the polynomial approximation.\\ {{:​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_datapoints.png?​nolink&​400|}} 
 +  - A 3rd order polynomial approximation can be obtained from the trendline of the x-y scatter plot of the data.\\ {{:​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_polynomial.png?​nolink|}}\\ ​
 <note important>​The number of significant digits of the coefficients of the polynomial equation is crucial to the accuracy of the approximation. However, the CN0503 also has an 80-character limit for each command. It is recommended to use a **3 decimal digit scientific notation** for the coefficients.\\ {{ :​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_scinotation.png?​nolink&​400 |}}</​note>​ <note important>​The number of significant digits of the coefficients of the polynomial equation is crucial to the accuracy of the approximation. However, the CN0503 also has an 80-character limit for each command. It is recommended to use a **3 decimal digit scientific notation** for the coefficients.\\ {{ :​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_scinotation.png?​nolink&​400 |}}</​note>​
-The polynomial approximation is applied to the CN0503 using the **DEFX ​INS0** or **DEFX ​INS1** command (See the [[resources:​eval:​user-guides:​eval-adicup3029:​reference_designs:​demo_cn0503|Software User Guide]] for more details on this). ​With this, the CN0503 will now calculate ​quinine concentration ​from real-time intensity samples.\\ {{ :​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_commandins.png?​nolink&​600 |}}+The polynomial approximation is applied to the CN0503 using the **DEFX ​INS1** or **DEFX ​INS2** command (See the [[resources:​eval:​user-guides:​eval-adicup3029:​reference_designs:​demo_cn0503|Software User Guide]] for more details on this). ​Once set, the INS1 and INS2 values represent the approximated ​quinine concentration\\ {{:​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​fl_inscmd.png?​nolink&​600|}}
 ===== Reference Links ===== ===== Reference Links =====
   * [[resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503|Hardware User Guide]]   * [[resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503|Hardware User Guide]]
   * [[resources:​eval:​user-guides:​eval-adicup3029:​reference_designs:​demo_cn0503|Software User Guide]]   * [[resources:​eval:​user-guides:​eval-adicup3029:​reference_designs:​demo_cn0503|Software User Guide]]
   * {{ :​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​cn0503_gui_quick_start_guide.docx | Quick Setup Guide }}   * {{ :​resources:​eval:​user-guides:​circuits-from-the-lab:​cn0503:​cn0503_gui_quick_start_guide.docx | Quick Setup Guide }}
resources/eval/user-guides/circuits-from-the-lab/cn0503/fluorescence.txt · Last modified: 21 Jan 2022 21:46 by Angelo Nikko Catapang