Project plan ready.

docs/comparision assays/comparision.tex

@@ -0,0 +1,134 @@
+\documentclass{article}
+
+% Geometry stuff
+\usepackage[head=24pt,a4paper,lmargin={2.5cm},rmargin={2.5cm},tmargin={2.5cm},
+bmargin={2.5cm}]{geometry}
+
+% Tables
+\usepackage{tabularx}
+
+% Images
+\usepackage{graphicx}
+
+% Fancyhdr
+\usepackage{fancyhdr}
+
+\fancyhead[LO,LE]{\includegraphics[scale=0.2]{./fig/uppsla_university.png}}
+
+\fancyhead[RO,RE]{Comparision of Assays}
+
+\fancyhead[CO,CE]{\today}
+
+\fancyfoot[R]{Elmar van Rijnswou}
+
+\fancyfoot[L]{Maximilian Stiefel}
+
+% For links
+\usepackage{hyperref}
+
+% For floating
+\usepackage{float} 
+
+% For special characters
+\usepackage{textcomp}
+
+\begin{document}
+\pagestyle{fancy}
+
+\section{Alexa Fluor\textregistered 647 dye}
+
+\begin{figure}[H]
+	\centering
+	\includegraphics[width=0.8\textwidth]{./fig/spectrum_alexa_647_laser_635}
+	\caption{Screenshot from the Thermo Fisher tool with the targeted laser.}
+	\label{fig:alexa_647}
+\end{figure}
+
+\subsection{Overview of Coponents}
+\begin{table}[H]
+\centering
+\begin{tabular}{lll}
+\hline
+\textbf{Product}                               & \textbf{Distributor} & \textbf{Price} \\\hline
+Red Laser Diode 635 nm +/- 5 nm, 33 mA, 2.2 V  & Farnell         & 179.67 SEK     \\
+Red Laser Diode 635 nm +/- 10 nm, 55 mA, 2.2 V & Aliexpress      & 2.5 \$ = 22.43 SEK \\
+Photodiode BPW34                               & Farnell         & 7.48 SEK       \\
+Longpass filter 675 nm                         & Edmund Optics   & 89 \$ = 798.33 SEK \\
+Longpass filter 670 nm                         & Aliexpress      & 45.79 \$ = 402.49 SEK \\\hline
+\end{tabular}
+\caption{Materials needed for the Alexa Fluor® 647 dye.}
+\label{tab:647}
+\end{table}
+\subsection{Laser Diode}
+A good laser diode is available at Farnell:\\
+\href{http://se.farnell.com/laser-components/2008352/laser-diode-635nm/dp/1272657?ost=laser+635+nm&categoryId=700000006112&searchView=table&iscrfnonsku=false}{http://se.farnell.com/laser-components/2008352/laser-diode-635nm/...}\\
+Cheaper diodes are available from China:\\
+\href{https://www.aliexpress.com/item/10-pcs-5mW-635nm-Orange-Red-TO18-5-6mm-N-type-Laser-Diode-LD-SANYO-DL/32622824538.html?spm=2114.01010208.3.322.KNKdbx&ws_ab_test=searchweb0_0,searchweb201602_3_10065_10068_10136_10137_10138_10060_10062_10141_10056_10055_10054_122_10059_10099_10103_10102_10096_10052_10053_10050_10107_10142_10051_10143_10084_10083_10080_10082_10081_10110_10111_10112_10113_10114_10078_10079_10073_10070_10123_10124,searchweb201603_2,afswitch_1,ppcSwitch_4,single_sort_0_default&btsid=b98573dc-6228-4b35-ad77-02e75b3fe435&algo_expid=3174f530-2df6-46b1-87c5-c36e2f9f58b0-38&algo_pvid=3174f530-2df6-46b1-87c5-c36e2f9f58b0}{https://www.aliexpress.com/item/10-pcs-5mW-635nm-Orange-Red-TO18-5-6mm-N-type-Laser-Diode-LD-SANYO-DL..}
+\subsection{Photodiode}
+The BPW34 is cheaply available at Farnell:\\
+\href{http://se.farnell.com/vishay/bpw34/photodiode-2na-900nm-rectangular/dp/1045425}{http://se.farnell.com/vishay/bpw34/photodiode-2na-900nm-rectangular/dp/1045425}\\
+One has to watch out as not all BPW34s have the same spectral sensitivity. This diode is also available cheaper in China.  
+\subsection{Filter}
+The filter can be obtained from Edmund Optics:\\
+\href{https://www.edmundoptics.com/optics/optical-filters/longpass-edge-filters/longpass-filters/64621/}{https://www.edmundoptics.com/optics/optical-filters/longpass-edge-filters/longpass-filters/64621/}\\
+Similar filters can be found in China:\\
+\href{https://www.aliexpress.com/item/Diameter-60mm-HB670-IR-Band-Pass-Filter-Long-Wavelength-Band-Pass-Filter/32766997403.html?spm=2114.01010208.3.10.iVA9gb&ws_ab_test=searchweb0_0,searchweb201602_3_10065_10068_10136_10137_10138_10060_10062_10141_10056_10055_10054_122_10059_10099_10103_10102_10096_10052_10053_10050_10107_10142_10051_10143_10084_10083_10080_10082_10081_10110_10111_10112_10113_10114_10078_10079_10073_10070_10123_10124,searchweb201603_2,afswitch_1,ppcSwitch_4,single_sort_0_default&btsid=882bb4cb-2a55-4d1b-8d9b-0348a7b8ec5f&algo_expid=ee21d12d-5045-4fab-93e1-0a0a214c0df0-1&algo_pvid=ee21d12d-5045-4fab-93e1-0a0a214c0df0}{https://www.aliexpress.com/item/Diameter-60mm-HB670-IR-Band-Pass-Filter-Long-Wavelength-Band-Pass-Filter/...}
+\begin{figure}[H]
+	\centering
+	\includegraphics[width=0.8\textwidth]{./fig/spectra_filter_china}
+	\caption{Chinese filters available from this distributer.}
+	\label{fig:chines_filter}
+\end{figure}
+Before ordering we definitely have to talk to Uwe to double check if this filter works. There is a huge variety of available filters. Both filters are usable for multiple devices as one can cut them. Both filters are circle shaped and have a diametel of 12.5 mm.  
+
+\section{Qdot\textregistered 800 streptavidin conjugate}
+
+\begin{figure}[H]
+	\centering
+	\includegraphics[width=0.8\textwidth]{./fig/spectrum_qdots_800_400}
+	\caption{Screenshot from the Thermo Fisher tool with 400 nm laser. I reality this might be a UV LED.}
+	\label{fig:qdots_800_400}
+\end{figure}
+
+\begin{figure}[H]
+	\centering
+	\includegraphics[width=0.8\textwidth]{./fig/spectrum_qdots_800_365}
+	\caption{Screenshot from the Thermo Fisher tool with 365 nm laser. I reality this might be a Blacklight LED.}
+	\label{fig:qdots_800_400}
+\end{figure}
+
+\subsection{Overview of Coponents}
+\begin{table}[H]
+\centering
+\begin{tabular}{lll}
+\hline
+\textbf{Product}                               	& \textbf{Distributor} 	& \textbf{Price} \\\hline
+UV LED 400 nm, 20 mA, 3.7 V			& Farnell		& 43.22 SEK	\\
+UV LED 400 nm, 20 mA, 3 V			& Aliexpress		& 0.05 \$ = 0.45 SEK \\
+UV LED 365 nm, 30 mA, 3.2 V			& Ebay			& 5 EUR = 47.8 SEK \\
+Photodiode BPW34                              	& Farnell         	& 7.48 SEK       \\
+Photodiode BPW34				& Aliexpress		& 0.281 \$ = 2.52 SEK \\
+Photodiode BPW34FS				& Farnell		& 8.63 SEK \\\hline
+\end{tabular}
+\caption{Materials needed for the Alexa Fluor® 647 dye.}
+\label{tab:647}
+\end{table}
+
+\subsection{LEDs}
+Two different types of LEDs are possible. Either UV LEDs, which are quite cheap in China:\\
+\href{https://www.aliexpress.com/item/100PCS-Purple-Color-5mm-Transparent-Water-ClearRound-Super-Bright-UV-LED-DIODE/32266780769.html?spm=2114.01010208.3.12.tra0j7&ws_ab_test=searchweb0_0,searchweb201602_3_10065_10068_10136_10137_10138_10060_10062_10141_10056_10055_10054_122_10059_10099_10103_10102_10096_10052_10053_10050_10107_10142_10051_10143_10084_10083_10080_10082_10081_10110_10111_10112_10113_10114_10078_10079_10073_10070_10123_10124-10111,searchweb201603_2,afswitch_1,ppcSwitch_5,single_sort_0_default&btsid=93ee4e21-8cbb-4573-8c94-fde0f528a3a4&algo_expid=a530b458-dbb3-4e8e-9b05-e6f5bf8dd6c4-1&algo_pvid=a530b458-dbb3-4e8e-9b05-e6f5bf8dd6c4}{https://www.aliexpress.com/item/100PCS-Purple-Color-5mm-Transparent-Water-ClearRound-Super-Bright-UV-LED-DIODE...}\\
+Or quite expensive in Sweden:
+\href{http://se.farnell.com/bivar/led3-uv-400-30/uv-led-3mm-30deg/dp/1057107}{http://se.farnell.com/bivar/led3-uv-400-30/uv-led-3mm-30deg/dp/1057107}\\
+The other option, which is the better one, from my POV, are blacklight LEDs. Those are not really easily available. But there are some from Italy:
+\href{http://www.ebay.de/itm/365nm-5-LED-UV-5mm-ULTRAVIOLETTI-ONDA-KURZ-ZWECKE-MEDICI-ULTRAVIOLETTE-STRAHLUNG-/121843052978?hash=item1c5e6971b2:m:mVQ-u99Iola62PpsoNnF26g}{http://www.ebay.de/itm/365nm-5-LED-UV-5mm-ULTRAVIOLETTI-ONDA-KURZ-ZWECKE-MEDICI-ULTRAVIOLETTE-STRAHLUNG-/121843052978?hash=item1c5e6971b2:m:mVQ-u99Iola62PpsoNnF26g}
+
+\subsection{Photodiode}
+The idea is to use a photodiode without any filter in this case. The filter is the most expensive part of the whole system. In the datasheet of the BPW34 one can read, that the diode works from \textbf{430 nm to 1100 nm}. This means, that possibly UV light with 400 nm or even 365 nm will not be received by this diode. We have to discuss this with Uwe or maybe even try it out. Datasheet of the BPW34:\\
+\href{http://www.farnell.com/datasheets/2046123.pdf}{http://www.farnell.com/datasheets/2046123.pdf}\\
+This photodiode is available cheaper from various sources e.g.:\\
+\href{https://www.aliexpress.com/item/Smart-Electronics-10pcs-lot-BPW34-Photodiode/32711869804.html?spm=2114.01010208.3.37.kEUjrU&ws_ab_test=searchweb0_0,searchweb201602_3_10065_10068_10136_10137_10138_10060_10062_10141_10056_10055_10054_122_10059_10099_10103_10102_10096_10052_10053_10050_10107_10142_10051_10143_10084_10083_10080_10082_10081_10110_10111_10112_10113_10114_10078_10079_10073_10070_10123_10124,searchweb201603_2,afswitch_1,ppcSwitch_5,single_sort_0_default&btsid=7135d04f-8309-410c-a0c5-9b6acfaec429&algo_expid=395c0e88-612b-46b8-bc3a-0ed4465fb75e-4&algo_pvid=395c0e88-612b-46b8-bc3a-0ed4465fb75e}{https://www.aliexpress.com/item/Smart-Electronics-10pcs-lot-BPW34-Photodiode/...}\\
+Another option is maybe the BPW34FS, which is equiped with a "daylight filter", which results another spectral range of sensitivity (\textbf{780 nm to 1100 nm}):
+\href{http://se.farnell.com/osram/bpw34fs/photodiode-ir-filter-950nm-60deg/dp/1212747}{http://se.farnell.com/osram/bpw34fs/photodiode-ir-filter-950nm-60deg/dp/1212747}
+
+
+\end{document}

docs/project plan/mydefs.tex

@@ -16,7 +16,7 @@
 \newcommand{\myauthorb}{Maximilian Stiefel (Maximilian.Stiefel.8233@student.uu.se)}
 \newcommand{\myauthorc}{}
 \newcommand{\myduedate}{2017-17-10 13:00}
-\newcommand{\mytutor}{Gemma Mestres (gemma.mestres@angstrom.uu.se), Masood Kamali-Moghaddam (masood.kamali@igp.uu.se)}
+\newcommand{\mytutor}{Gemma Mestres (gemma.mestres@angstrom.uu.se)}
 \newcommand{\mykeywords}{}
 \newcommand{\myperiod}{September 2016 - September 2017}
 \newcommand{\myrev}{0.2}

docs/project plan/project_plan.tex

@@ -95,13 +95,16 @@ bmargin={2.5cm}]{geometry}
 \rhead{\ifnum\value{chapter}>0 {\rightmark}\\\textcolor{gray}{\leftmark} \fi}
 \lfoot{}
 \cfoot{\ifnum\value{chapter}>0 \thepage \fi}
-\rfoot{{\textcolor{red}{DRAFT}}}
+\rfoot{}
 \setlength{\headheight}{1cm}
 
 \usepackage[autostyle]{csquotes}
 \usepackage[style=ieee,backend=bibtex]{biblatex}
 \addbibresource{literature.bib}
 
+% For gantt charts
+\usepackage{pgfgantt}
+
 \begin{document}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -139,12 +142,14 @@ bmargin={2.5cm}]{geometry}
 \end{figure}
 In figure \ref{fig:block} one can see a rough sketch of the system architecture, which is planned. The signal flow is from the left to the right. First the assay has to be excited, which is done by a voltage source connected to a light emitting diode (LED). This can also be another voltage controlled source of light. Hence this has TBD. The light source however is controlled by software (Microcontroller, µC), which is done by a simple e.g. transistor circuit. Using this approach has the advantage, that one can mix up the received signal to a higher band by switching the light source on and off with a rectangular signal of e.g. 1 kHz. By doing so one can suppress noise. In this case one simply compares the average value when turned on to the average value when turned off. The difference is the value one is looking for.  
 \newpar
-The emitted light has to be filtered. As the wavelengths in this case are in the nm region, a optical filter is needed. Behind the filter a photo diode is located, which converts the light signal to an electrical signal. This signal probably has to be processed in a analog way (e.g. amplification and filtering) before it is transfered in the digital world (analog-digital converter, ADC). In the digital world one has a lot of possibilities. The first idea was to transmit the data via bluetooth to a phone. As one egineering team member jumped off and another one can not contribute full-time the strategy has been changed to use a simple OLED instead as a UI. This can be extended by e.g. buttons.    
+The likelihood, that the emitted light has to be filtered is quite high. Hence one needs an optical filter. Behind the filter a photo diode is located, which converts the light signal to an electrical signal. This signal probably has to be processed in a analog way (e.g. amplification and filtering) before it is transfered in the digital world (analog-digital converter, ADC). In the digital world one has a lot of possibilities. 
+\newpar
+The UI will be a cheap OLED display from Chine, which can be extended by buttons. In a later revision maybe bluetooth can be used to transfer the data to a mobile device.     
 
 \section{Realization}
-The idea is to have a printed circuit board (PCB). On this board the light source as well as the sink shall be placed on the bottom side. On the top side one can mount the µC and the UI. Multiple PCBs shall be ordered, which either are having different light sources and sinks or which enable the attachement (soldering) of different light sources and sinks. A USB jack shall be used as power source. So one can easily use a power bank. 
+The idea is to have a printed circuit board (PCB) as main part of the device in the end. On this board the light source as well as the sink shall be placed on the bottom side. On the top side one can mount the µC and the UI. A USB jack shall be used as power source. So one can easily use a power bank or a laptop to operate the device.  
 \newpar
-The optical filter can be mounted with epoxy resin on the PCB. Spacing bolts can be used to attach the PCB on a plate, where one can find a mechanism to easily fix the blood probe chip. Futhermore a black box which one can put over the so far depicted structure, has to be designed. This black box supresses light (noise) from the environment. Mechanical sketches, preferably created with a 3D CAD software, have to be provided in a later revision of this document. The mechanics can be 3D printed in house.     
+The optical filter can be mounted with epoxy resin on the PCB. Spacing bolts can be used to attach the PCB to a bottom plate, where one can find a mechanism to easily fix the blood probe chip. Futhermore a black box which one can put over the so far depicted structure, has to be designed. This black box supresses light (noise) from the environment. Mechanical sketches, preferably created with a 3D CAD software, have to be provided in a later revision of this document. The mechanics can be 3D printed in house.     
 
 \section{Frabrication}
 The PCBs can be fabricated in China. This is an example of a manufacturer: \url{https://www.elecrow.com/10pcs-2-layer-pcb.html}. The lead time until one can actually work with designed PCBs is roughly three weeks including the assembling and soldering, which has to be done by the egineering subgroup. Moreover simpler PCBs can be etched at the university.    
@@ -174,21 +179,54 @@ It is so far quite hard to estimate the exact product price as a lot of choices
 % Next Steps
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \chapter{Next steps}
-\section{Interfacing with the Assay Team}
+\section{Interface to the Assay Team}
 \begin{figure}[H]
 	\includegraphics[width=\textwidth]{./fig/spectra.png}
 	\caption{Spectral characteristics of the two fluorescent dyes, which have been targeted so far.}
 	\label{fig:assays}
 \end{figure}
-The assay team has so far targeted two different products, which they want to use to generate fluoresence light emission depending on the concentration of the so-called NT-ProBNP. It is now the task of the egineering team to put the required hardware together for the given spectral features. The two main parts as already emphasized above are the light emission and the light reception. For each product one has to set up a series of experiments to play with different parameters. For the first attempts this only includes analog parts and an oscilloscope. The challenge is mainly, that we do not know so far    how much light will be emitted. Is it visible? Is it a few photons? Also we do not know how constant the light emission has to be: Do we need an extra controller for that? Many lasers for instance provide an internal receiving photodiode, which is highly coupled with the sending diode. So one can use a software controller to keep the light emission pecisely at one point. Moreover we do not know so far how dark it should be arround the sample. 
+The assay team has so far targeted two different products, which they want to use to generate fluoresence light emission depending on the concentration of the so-called NT-ProBNP. It is now the task of the egineering team to put the required hardware together for the given spectral features. The two main parts as already emphasized above are the light emission and the light reception. For each product one has to set up a series of experiments to play with different parameters. For the first attempts this only includes analog parts and an oscilloscope. The challenge is mainly, that we do not know so far    how much light will be emitted. Is it visible? Is it a few photons? Also we do not know how constant the light emission for exitation has to be: Do we need an extra controller for that? Many lasers for instance provide an internal receiving photodiode, which is highly coupled with the sending diode. So one can use a software controller to keep the light emission pecisely at one point. Moreover we do not know so far how dark it should be arround the sample. 
 
 \section{First Experiments}
-One needs to design a circuit with optics, which is delivering an analog voltage at the output, which is dependent on the concentration of NT-proBNP. To build this circuit one has to determine which components are used also one has to copare different standard approaches how to monitor a photo diode with an Opamp. The thing, which has to be figured out in the end is, which gain is required, that the maximum and minimum light emission is visible as an electrical signal. Also the maximum output voltage should be equal to the reference voltage and the minimum output voltage should be 0 V to get the highest resolution. To develop this circuit LTSpice will be used as well as KiCAD. Most likely this PCB will be etched within the university. As soon as these experiments work, one can start working with a microcontroller. 
+One needs to design a circuit with optics, which is delivering an analog voltage at the output, which is dependent on the concentration of NT-proBNP. To build this circuit one has to determine which components are used also one has to copare different standard approaches how to monitor a photo diode with an Opamp. The thing, which has to be figured out in the end is, which gain is required, that the maximum and minimum light emission is visible as an electrical signal. Also the maximum output voltage should be equal to the reference voltage and the minimum output voltage should be 0 V to get the highest resolution according to signal processing theory. This requirements might result in more than one amplification stage. To develop this circuit LTSpice will be used as well as KiCAD. Most likely this PCB will be etched within the university. As soon as these experiments work, one can start working with a microcontroller. 
 \newpar
 The experiments can be carried out together with the biomedical colleagues in a dark room with and oscilloscope and a signal generator. Maybe three different circuits will be put on one PCB to make a simultaneous reception possible.  
 
 \section{Lot of Programming}
-As soon as we found an essay and a corresponding analog circuit, which works a microcontoller will be chosen and everything will be put together on one board. This microcontroller could be the NRF52832, MSP432 or a simple ATmega328P. The data has to be sampled and some calculations have to be done. Finally the data has to be displayed on an OLED. One important requirement for the whole team is, that the device is small as it has to be transported to Eindhoven for the competition in december.  
+As soon as we found an essay and a corresponding analog circuit, which works a microcontoller will be chosen and everything will be put together on one board. This microcontroller could be the NRF52832, MSP432 or a simple ATmega328P. The data has to be sampled and some calculations have to be done. Finally the data has to be displayed on an OLED. One important requirement for the whole team is, that the device is small as it has to be transported to Eindhoven for the competition in december.   
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Gantt
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\chapter{Gantt}
+\begin{figure}[h]
+	\centering
+	\begin{ganttchart}
+		[
+		hgrid, 
+		vgrid,
+		x unit = 0.5cm,
+		y unit chart = 0.6cm
+		]{1}{23}
+		\gantttitle{Calendar Weeks}{23} \\
+		\gantttitlelist{14,...,36}{1}\\ 
+		\ganttbar{Determine Assay}{1}{2}\\	
+		\ganttlinkedbar{Design Simple PCB}{3}{4}\\
+		\ganttlinkedbar{Experiments}{5}{9}\\	
+		\ganttmilestone{Analog Parm. set}{9}\\
+		\ganttbar{Design final HW}{10}{11}\\
+		\ganttlinkedbar{Design Mechanics}{12}{13}\\
+		\ganttlinkedbar{Write SW}{14}{17}\\
+		\ganttlinkedbar{Test and Integration}{18}{19}\\
+		\ganttbar{Buffer}{20}{21}\\
+		\ganttbar{Competition Prep.}{22}{23}\\
+		\ganttmilestone{Competition}{23}
+		\ganttlink{elem2}{elem4}
+		\end{ganttchart}
+	\caption[]{Gantt Chart}  
+	\label{fig:zeitplan}  
+\end{figure}
+This chapter is about the current time plan. The experiments are mainly to figure out the correct amplifier design and to determine if the desired technique works at all. As soon as the parameters for the amplifier are set the device design phase starts. And the final hardware is designed. At the end there is a buffer of three weeks if anything goes wrong. If we can stick to this ambitious timeplan we may take this period off. The last two weeks are reserved for preparing the competition as e.g. a presentation and a stand have to be prepared.  
 
 \printbibliography[heading=bibintoc]