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Data acquisition and data analysis custom code for non-invasive Raman micro-spectroscopy application tracking D2O in living roots
software
posted on 2021-06-21, 13:11 authored by Flavius
C. Pascut, Kevin F. Webb**********************
* Data Acquisition *
**********************
RamanSoftv1_line scan was developed in Visual C# 2008 Express Edition version 9.0.30729.1 SP with Net Framework 3.5 SP1 under Windows XP professional version 5.1.2600 SP3 build 2600.
The entire source code can be found inside the "DataAcquisition/RamanSoftv1_linescan" directory.
To run the software two additional external dependencies are required to be installed on the same host PC:
1) ANDOR SOLIS + Andor SDK
SOLIS version: 4.2230007.0
SDK version: 2.94.30007.0
ATMCD32CS.dll supplied with the Andor software has to be added to the resources manager inside C# IDE
2) Prior scientific software Version 1.78.0.0
Interop.PriorLib.dd supplied with the Prior software has to be added to the resources manager inside C# IDE
An example.dat file is provided as a demo that contains a raw Raman spectrum.
The file is recognised by the Raman data acquisition program and it will display the content by pressing the "Add Spectrum" button inside the software.
For more information, feel free to contact Flavius.Pascut@nottingham.ac.uk
*******************
* Data Analysis *
*******************
DataAnalysis.m is a Matlab script created in Matlab R2018a version 9.4.0.813654.
It takes the input of an ASC file (format generated by Andor SOLIS) and performs the following data analysis procedures:
1) Cosmic rays removal
2) Laser power fluctuation corrections
3) Background Subtraction
4) Gaussian Peak fitting
User instructions: copy the DataAnalysis directory including its content onto the C drive.
Run matlab and open the scrip.
Press run inside Matlab.
The script will run for few minutes then displaying the peak area results.
The script requires two additional functions to operate.
- Cosmic rays removal, this function was created by the author of this matlab script and has been provided in the same directory.
- The second function, Gaussian Peak fit can be found following this link https://www.mathworks.com/matlabcentral/fileexchange/23611-peakfit-m
Two data example files are provided d2o_out.asc representing a typical D2O wash out process AND d2o_in.asc representing a typical D2O wash in process.
These two data sets were acquired using Andor Solis version: 4.2230007.0 and saved as .asc
For more information, feel free to contact Flavius.Pascut@nottingham.ac.uk
* Data Acquisition *
**********************
RamanSoftv1_line scan was developed in Visual C# 2008 Express Edition version 9.0.30729.1 SP with Net Framework 3.5 SP1 under Windows XP professional version 5.1.2600 SP3 build 2600.
The entire source code can be found inside the "DataAcquisition/RamanSoftv1_linescan" directory.
To run the software two additional external dependencies are required to be installed on the same host PC:
1) ANDOR SOLIS + Andor SDK
SOLIS version: 4.2230007.0
SDK version: 2.94.30007.0
ATMCD32CS.dll supplied with the Andor software has to be added to the resources manager inside C# IDE
2) Prior scientific software Version 1.78.0.0
Interop.PriorLib.dd supplied with the Prior software has to be added to the resources manager inside C# IDE
An example.dat file is provided as a demo that contains a raw Raman spectrum.
The file is recognised by the Raman data acquisition program and it will display the content by pressing the "Add Spectrum" button inside the software.
For more information, feel free to contact Flavius.Pascut@nottingham.ac.uk
*******************
* Data Analysis *
*******************
DataAnalysis.m is a Matlab script created in Matlab R2018a version 9.4.0.813654.
It takes the input of an ASC file (format generated by Andor SOLIS) and performs the following data analysis procedures:
1) Cosmic rays removal
2) Laser power fluctuation corrections
3) Background Subtraction
4) Gaussian Peak fitting
User instructions: copy the DataAnalysis directory including its content onto the C drive.
Run matlab and open the scrip.
Press run inside Matlab.
The script will run for few minutes then displaying the peak area results.
The script requires two additional functions to operate.
- Cosmic rays removal, this function was created by the author of this matlab script and has been provided in the same directory.
- The second function, Gaussian Peak fit can be found following this link https://www.mathworks.com/matlabcentral/fileexchange/23611-peakfit-m
Two data example files are provided d2o_out.asc representing a typical D2O wash out process AND d2o_in.asc representing a typical D2O wash in process.
These two data sets were acquired using Andor Solis version: 4.2230007.0 and saved as .asc
For more information, feel free to contact Flavius.Pascut@nottingham.ac.uk
Funding
Direct visualisation of epithelial fluid transport at the subcellular scale
Biotechnology and Biological Sciences Research Council
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