Using AGScan - MulCyber
Contents
1. cssssssssssssssssscssscsccccsssscccsccssssscccccessssssccccesessscccccessesscsssscsssescecesecoosess 19 MAI Simulator v0 5 User Manual page 3 Sigenae July 2007 Edition Illustration Index Illustration 1 Tabbed Me nu cece cree eee eem eene nennen antes nnn aia e ren 5 Illustration 2 Progress bar and launch DUttON eee eee eee eene 5 Illustration 3 General ParaMeteLS ccc eee eee tee eee eee saan A ane een rede nne neennnn nennen 6 lllustration 4 Border Size eet ede ded ees aha eu en Sie dae 7 Illustration 5 Grid ParaMetels rein enne Eaa EE 8 Illustration 6 Spot parameters ssssssssssnm Hem hen nm mene herren rene 10 Illustration 7 Noise parameters sssssssssn meh ene hne 12 Illustration 8 SpIKes u i eiit ee vhs Ree ia acia 13 Illustration 9 Fast ViOW 0 mme hne nnne nnnner rennen nere 14 Illustration 10 Quantification file example 1 sssesennm mnn 15 Illustration 11 Quantification file example 2 sssssm HH HH 15 Illustration 12 Gaussian Curve ssssessseseesseeenenenenmmenn menm nennen rh nene rh nennen e 16 Illustration 13 Shape repartition before sssssssssse mmm rne 17 Illustration 14 Shape repartition after cece etter renee seeders earns mme 18 MAI simulator Plugin User Manual page 4 20 Sigenae July 2007 Edition Il Introduction Micro Array Image Simulator MAI simula2. 0 Validate L uc No running process Illustration 5 Grid parameters 1 Grid dimensions e Number of lines This is the number of block lines e Number of columns This is the number of block columns e Number of meta lines This is the number of lines in one block e Number of meta columns This is the number of columns in one block e Space inter lines in pixels This is the gap between block lines e Space inter columns in pixels This is the gap between block columns e Space inter meta lines in pixels This is the gap between lines in each block e Space inter meta columns in pixels This is the gap between columns in each block e Pixel size in p meters This is the pixel height and width MAI simulator Plugin User Manual page 8 20 Sigenae July 2007 Edition 2 Grid noises For not perfectly regular grids it is possible to introduce three kinds of noise e Angle in degrees Rotates the grid e Enlargement in pixels Enlarge the grid length e Block shift in pixels Make a random shift on the grid blocks You must give two values for each shift side horizontal and vertical the mean and the standard deviation More explanations are given in the Noises and random chapter MAI simulator Plugin User Manual page 9 20 1 Sigenae a MicroArray Image Simulator lek July 2007 Edition General Spot Grid Noise Spikes FastView rExpr
3. Tabbed menu Amp Base name for images test Number of channels per image Number of generated images Illustration 1 Tabbed Menu The launch button Validate and the progress bar are located at the bottom of the pane Progression zx Validate x 1 1 Drawing spots Illustration 2 Progress bar and launch button MAI simulator Plugin User Manual page 5 20 cite D ud Sigenae July 2007 Edition Il Parameter Setting The chapter explains how to set the different parameter fields before launching the process 1 General MicroArray Image Simulator ax General Spot Grid Noise Spikes FastView r Working directory tmp Base name for images Test 6 r Number of channels per image r Number of generated images Border size pix s 100 cal Validate Us Siz No running process Illustration 3 General parameters The general tab enables to specify e Working directory This is the directory where all output files will be saved e Number of channels The number of channels of your experiments between 1 and e Number of images The number of experiments you want to generate between 1 and e Base name All images and quantification files names will start with the base name For example if you choose a 3 channels 2 images experiment with Test as base n
4. Program or a portion of it either verbatim or with modifications and or translated into another language Hereinafter translation is included without limitation in the term modification Each licensee is addressed as you Activities other than copying distribution and modification are not covered by this License they are outside its scope The act of running the Program is not restricted and the output from the Program is covered only if its contents constitute a work based on the Program independent of having been made by running the Program Whether that is true depends on what the Program does 1 You may copy and distribute verbatim copies of the Program s source code as you receive it in any medium provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty keep intact all the notices that refer to this License and to the absence of any warranty and give any other recipients of the Program a copy of this License along with the Program You may charge a fee for the physical act of transferring a copy and you may at your option offer warranty protection in exchange for a fee 2 You may modify your copy or copies of the Program or any portion of it thus forming a work based on the Program and copy and distribute such modifications or work under the terms of Section 1 above provided that you also meet all of these conditions a You must cause the modified files to carry
5. ShapeNameSpot derived from Spot After that two abstract methods getlmageSpot and deformate must be implemented Then the java file must be compiled and the class file put in the plugins directory of your Image install Finally the MAIS parameters properties file must be updated by adding a new spot shape name to the shapes line shapes Circle Gaussian Donut ShapeName where ShapeName is the new shape model If a model is to be removed just remove its name from the list Example removing the Circle shape shapes Gaussian Donut ShapeName The user interface evolves with the shape names provided in the shapes line of the MAIS parameters properties file User interface before Shape repartition Circle Spot Gaussian Spot 4 Illustration 13 Shape repartition before MAI simulator Plugin User Manual page 17 20 Pte SY Sigenae July 2007 Edition User interface after adding Custom and Donought shapes Shape repartition Circle Spot 69 Gaussian Spot C3 a Custom Spot 3 Donought Spot C3 Illustration 14 Shape repartition after MAI simulator Plugin User Manual page 18 20 icm D ud Sigenae July 2007 Edition GNU GENERAL PUBLIC LICENSE Version 2 June 1991 Copyright C 1989 1991 Free Software Foundation Inc 51 Franklin St Fifth Floor Boston MA 02110 1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document but changing it is not al
6. all For example if a patent license would not permit royalty free redistribution of the Program by all those who receive copies directly or indirectly through you then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Program If any portion of this section is held invalid or unenforceable under any particular circumstance the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims this section has the sole purpose of protecting the integrity of the free software distribution system which is implemented by public license practices Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system it is up to the author donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License MAI simulator Plugin User Manual page 19 20 cite D ud Sigenae July 2007 Edition 8 If the distribution and or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces the original copyrig
7. and the standard deviation Standard deviation Mean Illustration 12 Gaussian curve The values are taken between Mean 3 Sd and Mean 3 Sd For example if you give a mean value of 2 0 and a standard deviation of 1 0 the random values could be between 1 0 and 5 0 but in most of cases they will be between 1 0 and 3 0 2 Spot repartition The spot positioning in image uses a random system too In fact you give the system the percentage you want for each spot shape then according to the total number of spots and these percentages the software computes how much spots of each shape are needed For each spot it chooses the shape at random and re samples if the quantity needed has been MAI simulator Plugin User Manual page 16 20 Sigenae July 2007 Edition reached Finally you obtain exactly the percentages you have specified but the space repartition over images is randomly designed Adding spot shapes Three shape models have been developed in this Plugin Circle Gaussian and Donut MAI Simulator was designed in order to allow developers to easily add new ones without changing the code Each shape model implements an interface class the Spot class Examples can be found using the CircleSpot GaussianSpot and DonutSpot classes All the class names end with Spot and this is used by MAI Simulator to load them So if someone wants to develop a new shape model she or he has to create a new class named
8. generally NO WARRANTY 11 BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE THERE IS NO WARRANTY FOR THE PROGRAM TO THE EXTENT PERMITTED BY APPLICABLE LAW EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND OR OTHER PARTIES PROVIDE THE PROGRAM AS IS WITHOUT WARRANTY OF ANY KIND EITHER EXPRESSED OR IMPLIED INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU SHOULD THE PROGRAM PROVE DEFECTIVE YOU ASSUME THE COST OF ALL NECESSARY SERVICING REPAIR OR CORRECTION 12 IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER OR ANY OTHER PARTY WHO MAY MODIFY AND OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE BE LIABLE TO YOU FOR DAMAGES INCLUDING ANY GENERAL SPECIAL INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES MAI simulator Plugin User Manual page 20 20
9. them these terms so they know their rights We protect your rights with two steps 1 copyright the software and 2 offer you this license which gives you legal permission to copy distribute and or modify the software Also for each author s protection and ours we want to make certain that everyone understands that there is no warranty for this free software If the software is modified by someone else and passed on we want its recipients to know that what they have is not the original so that any problems introduced by others will not reflect on the original authors reputations Finally any free program is threatened constantly by software patents We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses in effect making the program proprietary To prevent this we have made it clear that any patent must be licensed for everyone s free use or not licensed at all The precise terms and conditions for copying distribution and modification follow TERMS AND CONDITIONS FOR COPYING DISTRIBUTION AND MODIFICATION 0 This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License The Program below refers to any such program or work and a work based on the Program means either the Program or any derivative work under copyright law that is to say a work containing the
10. 1521 43681 676 225 256 58081 169 15625 Chan2 Chan3 92416 30976 61009 61009 44100 44100 20164 20164 6561 6561 2116 2116 26569 26569 100 100 441 441 57600 93636 49 49 3721 3721 61009 61009 484 484 441 441 3136 3136 64 64 121 121 16 16 5929 5929 70225 70225 16384 16384 30625 30625 289 289 Chan4 61009 44100 20164 6561 2116 26569 100 441 40401 49 3721 61009 484 441 3136 121 16 5929 70225 16384 30625 289 page 15 20 Sigenae July 2007 Edition Ill Noises and random values Random number generation is very useful to produce a realistic set of images Nearly all kinds of noise have a random part This chapter explains how random is used in MAI Simulator DNA chips images are known to contain many kinds of noise Noise in experiment chain Noise in MAlSimulator Systematic position errors because of pin deformations Block shift noise Non systematic position error Spot shift noise Orientation variation Angle noise Deformation of the initial spotting schema due to soft Enlargement noise support material membrane technology Background noise due to quality of scan General and local noises Background noise due to dusts Scratch and dust noise 1 Mean value and standard deviation Some random values are generated using the Gaussian distribution This is why often you have to give two values in the user interface of MAI Simulator the mean value
11. a aeaa soustavedcestaesuncsescsdeshesetes asdececcdbesesuecesuesseeesssvsseesesdecuesecsouvacees 6 GENERAL ptr cd a I ae cna LI M I LI 6 AS MED O 8 VE ERAS SO IR ERE Rc 8 2 Grid TOUS ES au ecco Sete e ere eo ERR ecpdno cuve duas epa dre inue ven pee dewetbnncridcesilyecdeetebuacdsdedessarucueveuuboasndesnsbelbeces 9 tM ETC EUER 10 1 General orien IN 10 2 SPOLNOISCS ioi vereor tene ute Aure Erde E EA atr epa eU fee inea AEA abe 11 NN 12 QT TAMBIEN 12 2 Local noise Not implemented in the July 2007 version sse 12 3 Scratch amp dust NOIUSEC cccccccccccccccccccssssssccccscsssssscccssessnsssesessssscescsssssssescssssssseseesessnssecsenssnsssesessssssseseeseseeseseuss 12 SSS PIRES MEN P TI 13 us Cuius 14 FARBSULM BIB 2355 305555255 U 15 III NOISES AND RANDOM VALUE G cssssssssssssssssscssssccscccssssccscccsssssssccessssssccecscsssseecsecsessscsceessescesseesesscees 16 1 MEAN VALUE AND STANDARD DEVIATION ssssccccesssssseecesesssseecccessssseeeccesssseeeccesenseeeeccensaeeeceeeesaaeeeceseesseeceeeesseeeeseeeaes 16 2 POD REPARTITION s 050cheseadecdencceasageace cays ERE RECO RU ERE ERE eave snceiaeseuageededcavss 00ueceaes osudouetes dan ERAN LAS REE REY EE essuscceeuoaeeseseens 16 GNU GENERAL PUBLIC LICENGE
12. ame output files will be Test1_1 tiff Test1_2 tiff Testl 3 tiff the 3 channels of the first image MAI simulator Plugin User Manual page 6 20 Paa A Sigenae July 2007 Edition Test2_1 tiff Test2_2 tiff Test2_3 tiff the 3 channels of the second image Test1 txt the quantification file for the first image Test2 txt the quantification file for the second image e Border size in pixels You can set the size of the image borders e 0 000 o o B o e 0000 LJ 0000 LAN NE o e LA E E 0 ee e Illustration 4 Border size NB Be careful when defining the border size for rotated images MAI_simulator Plugin User Manual page 7 20 icm D ud Sigenae July 2007 Edition 2 Grid a MicroArray Image Simulator 50X General Spot Grid Noise Spikes Fastview Grid dimensions Number of lines 12H Number of columns 4H Number of metalines 258 Number of metacolumns 25H Space between lines pix 205 Space between columns pix 20H Space between metalines pix 0H Space between metacolumns pix 0r Pixel sizequm 25E r Other noises L j 3 Angle deg C Random deviation 90 60 30 0 30 60 90 Enlargement pix C Random deviation 90 60 30 0 30 60 90 Horizontal blocshiftipix C Random deviation 0 30 60 90 Vertical blocshift pix C Random deviation lica 0 30 60 90
13. an PI Sigenae July 2007 Edition MAI simulator Micro Array Image Simulator USERS MANUAL Version 0 5 July 2007 Edition Nicolas Mary amp Christophe Klopp Copyright 2007 SIGENAE INRA Permission is granted to copy distribute and or modify this document under the terms of the GNU Free Documentation License Version 1 2 or any later version published by the Free Software Foundation with the Invariant Sections being just Background no Front Cover Texts and no Back Cover Texts A copy of the license is included in the section entitled GNU Free Documentation License at the end of this manual MAI Simulator v0 5 User Manual page 1 Paa ay Sigenae July 2007 Edition Revision table Version Date Major modifications Author s 0 1 June 6 2007 First draft N Mary 0 2 June 27 2007 First revision Ch Klopp 0 3 June 27 2007 Second revision N Mary 0 4 July 11 2007 Third revision Ch Klopp 0 5 July 11 2007 Fourth revision N Mary Acknowledgment wrote this guide in English having the aim to give access to MAI simulator to the largest possible scientific community But English is not my mother language so any remark about the orthography or the grammar is welcome MAI Simulator v0 5 User Manual page 2 cite D d Sigenae July 2007 Edition INDEX T INTRODUCTION Pe rn ES 5 M PARAMETER SETTING e
14. e number of fractals and their size During the process fractals will be placed randomly on the images 3 Scratch amp dust noise You can also put scratch and dust noises on your images These aim to simulate the micro dusts on the glass slides You could choose two shapes ovals and or lines and how much of each you want Then you must customize them specifying their width and height Like with local noise scratches and dusts will be placed randomly on the images MAI simulator Plugin User Manual page 12 20 Sigenae July 2007 Edition 5 Spikes O MicroArray Image Simulator nx General Spot Grid Noise Spikes Fastview Pepe ppp PPPPPPPPPPP on eereerererere H DH BHBHBHBmpPmDpDPrm NJ EG p p p pp p p P DI OD 9O9 WA WwN p b LLANAMAWNEP OEE ps ps po o po PE RrrrbrerraAre PRPRERPRPRRPRRRRR PEREEPRPRRRRRRER Validate zs f No running process Illustration 8 Spikes Spikes are spots set to the maximum intensity value In fact they are used to indicate a position on the grid like tags They are very helpful in the alignment process For example they can be used to locate the upper left corner of each block of the grid You can specify a list of spikes giving their coordinates with the following format ijk c1f c2 c3 f means optional iis the line index of the block jis the column index of the block k is the li
15. ed so long as such parties remain in full compliance 5 You are not required to accept this License since you have not signed it However nothing else grants you permission to modify or distribute the Program or its derivative works These actions are prohibited by law if you do not accept this License Therefore by modifying or distributing the Program or any work based on the Program you indicate your acceptance of this License to do so and all its terms and conditions for copying distributing or modifying the Program or works based on it 6 Each time you redistribute the Program or any work based on the Program the recipient automatically receives a license from the original licensor to copy distribute or modify the Program subject to these terms and conditions You may not impose any further restrictions on the recipients exercise of the rights granted herein You are not responsible for enforcing compliance by third parties to this License 7 If as a consequence of a court judgment or allegation of patent infringement or for any other reason not limited to patent issues conditions are imposed on you whether by court order agreement or otherwise that contradict the conditions of this License they do not excuse you from the conditions of this License If you cannot distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations then as a consequence you may not distribute the Program at
16. essed saturated and deformated spots Expression rate s 25 50 75 100 NI Saturation rate s 25 50 75 100 Deformation rate 3 25 50 75 100 rShifted spots Shift rated 0 25 50 75 100 Shift value pix 50 25 0 25025 7 a Random deviation for shift value pix 50 25 0 zs Ell rShape repartition Circle Spot 69 100 Gaussian Spot 5 9 Custom Spot 3 6 Donought Spot 3 rSpot size Spot height pix 20H Spot width pix 20 Shift between channels um rm S SS 0 Validate d sf No running process Illustration 6 Spot parameters General Once grid parameters have been set you have to decide what you want the spots to look like e Expression rate Sets the rate of expressed spots e Saturation rate Sets the rate of saturated spots e Deformation rate 96 Sets the rate of distorted spots e Shape repartition 96 Here you will choose a percentage for each shape model The total must be 100 unless the process can t be launched e Spot size in pixels You must also set the spot width and height MAI simulator Plugin User Manual page 10 20 Sigenae July 2007 Edition 2 Spot noises e Spot shift in pixels Make a random shift on spots You must give two values the mean and the standard deviation More explanations a
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19. ile 1 All Normall txt PixelSize 25 ImageOrigin 0 0 In dex X 8925 9425 9925 10425 10925 11400 11900 12400 12900 13400 13900 14425 8875 9375 9875 10375 10875 11375 11875 12375 Y 5525 5550 5600 5650 5700 5725 5775 5825 5875 5900 5950 6000 6025 6050 6100 6150 6200 6225 6275 6325 File 4 Sinus Normal3 txt PixelSize 25 ImageOrigin 0 0 Index t C Ov UP QD ND 11 12 13 14 15 16 18 19 20 21 22 23 24 x 8600 9100 9575 10075 10575 11000 11575 12100 12600 13100 13600 14100 8550 9050 9550 10050 10550 11050 11550 12075 12575 13075 13575 14075 T 5950 5975 6000 6050 6075 6100 6150 6200 6225 6250 6300 6325 6475 6475 6500 6500 6575 6625 6650 6675 6725 6750 6800 6825 ee MAI simulator Plugin User Manual HP HH RP RRP RP RP RP BP RP RP RP RE RE RR al a RRE 1 BO MO MO NO MO MO NJ NJ EB RP RRP PP RP RP RP RP ee WOH HAM 4 CQ IN EE PRR Nro PR 2 3 4 5 6 7 8 Illustration 10 Quantification file example 1 a PRR RP RRP RRR BP RP RP RP RP RRP EP RP RP RR RR 1 Illustration 11 INNNNNNNNNNNNEBP RBBB BBB RBBB Quantificai 10 C O Ur i QN c 10 Chanl 49 61009 44100 20164 6561 2116 26569 100 441 1849 49 3721 61009 484 441 3136 64 121 16 5929 70225 16384 30625 289 tion file example 2 Chanl 27556 3721 56169 144 45369 44521 32400 85756 169 225 676 361
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21. ne index of the spot in the block lis the column index of the spot in the block c1 c2 c3 are the channel indexes you must give one at least MAI simulator Plugin User Manual page 13 20 Paa A Sigenae July 2007 Edition 6 Fastview When MAI_Simulator has ended producing the tif files 16bits one file per channel the user can visualize the upper left corner of the generated images using the fast view panel He can choose the image he wants to check in the drop down list O MicroArray Image Simulator nx General Spot Grid Noise Spikes Fastview e o o TT e080 Test 7 11 ill Test 7 1 1 i Test_7_1_2 Validate L 1 1 Complete Illustration 9 Fast view MAI simulator Plugin User Manual page 14 20 7 Result file Sigenae July 2007 Edition MAI_Simulator generates images on one side and quantification files on the other The quantification files contain the random channel intensities for each channel of the image The examples presented hereunder correspond to single and a four channel images These files have several columns Index spot index X and Y location in micro meters of the spot center on image R C MR MC bloc row bloc column spot row and spot column within the bloc ChanX X channel intensity The result file is used to evaluate the quantification accuracy of microarray image analysis tools Creator ImageJ MAIS Plugin Creator ImageJ MAIS Plugin F
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23. prominent notices stating that you changed the files and the date of any change b You must cause any work that you distribute or publish that in whole or in part contains or is derived from the Program or any part thereof to be licensed as a whole at no charge to all third parties under the terms of this License C If the modified program normally reads commands interactively when run you must cause it when started running for such interactive use in the most ordinary way to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty or else saying that you provide a warranty and that users may redistribute the program under these conditions and telling the user how to view a copy of this License Exception if the Program itself is interactive but does not normally print such an announcement your work based on the Program is not required to print an announcement These requirements apply to the modified work as a whole If identifiable sections of that work are not derived from the Program and can be reasonably considered independent and separate works in themselves then this License and its terms do not apply to those sections when you distribute them as separate works But when you distribute the same sections as part of a whole which is a work based on the Program the distribution of the whole must be on the terms of this License whose permissions for other licensees extend to the e
24. re given in the Noises and random chapter e Inter channel shift in pixels In mono channel case this has no effect In multi channel case this noise is not applied to the first channel image but to all others Make a random shift on the whole channel image You just give one value here the standard deviation In fact the mean is set to 0 More explanations are given in the Noises and random chapter MAI simulator Plugin User Manual page 11 20 pte D ud Sigenae July 2007 Edition a MicroArray Image Simulator nx General Spot Grid Noise Spikes Fastview r General Noise Add Yes No ja 25 50 75 100 Value rLocal Noise O Add Yes No Number 5H Sizewix 5E rScratch amp Dust Noise C Add Yes No Number of lines 5r width 5H Height 5 Number of ovals 5 Height 5H Width sH validate Um No running process Illustration 7 Noise parameters 1 General noise Here you can set a background noise value This will add a salt and pepper noise all over the images The value sets the noise density a high value means a high density 2 Local noise Not implemented in the July 2007 version Local noise refers to fractal phenomenas If you want to add this kind of noise you must choose th
25. tor has been developed in order to generate micro array images These images are simulated thanks to several user defined parameters Generating these images aims at creating test sets for image quantification software For each run the simulator generates sets of images and the corresponding quantification files These quantification files can be used as references while analyzing and comparing microarray image quantification software Parameters are sorted in five categories General parameters Grid parameters Spot parameters Noise parameters Spike ins General parameters define the naming schema of the created files and the directory in which the file are generated The grid parameters define the grid configuration elements such as number of meta rows meta columns rows and columns The spot parameters determine the spot shape expression level saturations and deformation In order to stick to real data users are able to add different kinds of noises thanks to noise parameters The spike ins tab enables the user to define the location of saturated spots in the image The spots can be used in the grid positioning process or in quantification normalization process When all parameters fields are set the user can launch the process and then take a look at the generated images and quantification files i MicroArray Image Simulatc General Spot Grid Noise Spikes FastView Working directon
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