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imagesci and imagesource user manual all possible care has been taken in the preparation of this publication but spectronics corporation accepts no liability for any inaccuracies that may be found spectronics corporation reserves the right to make changes without notice both to this publication and to the product that it describes no part of this publication may be reproduced stored in a retrieval system or transmitted in any form or by any means electronic mechanical photocopying recording or otherwise without the prior permission of the copyright owner published by spectronics corporation © synoptics limited 2004[close]
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spectronics corporation 959 brush hollow road p box .o westbury new york 11590 tel 1-800-274-8888 fax 1-800-491-6868 website www.spectroline.com[close]
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contents introduction and initial setup introduction imagesci overview connecting up software overview imagesource imageaide summary the system 1 1-1 1-2 1-2 1-2 1-3 1-3 1-4 1-4 getting started with imagesci 2 switching on 2-1 capturing an image from the camera 2-3 inserting the sample 2-3 capturing an image using automatic exposure 2-4 capturing an image from live video 2-5 capturing a single image with an exposure longer than five seconds 2-7 capturing a series of images 2-8 capturing an image with extended dynamic range 2-11 analyzing the image 2-11 hints 2-12 starting imagesource 2-12 logging in 2-13 displaying the image capture toolbox 2-13 image display 2-13 saturation detection 2-13 moving on 2-15 using imagesource 3 working with configurations 3-1 imagesci and imagesource user manual contents-1[close]
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contents user and system default configurations 3-1 selecting a configuration 3-2 creating and saving configurations 3-2 deleting a configuration 3-3 promoting a user configuration 3-4 capturing images from the camera 3-5 capturing an image from live video 3-6 capturing a single image 3-6 capturing images using series capture 3-7 capturing images using auto exposure 3-10 using edr extended dynamic range 3-10 using neutral field correction nf 3-11 adjusting display conditions 3-15 using the image window display controls 3-15 using the histogram window to control the image display 3-16 saving and loading image files 3-19 loading image files 3-20 creating a composite image multiplexing 3-22 manipulating images 3-24 image toolbar 3-25 original and processed images 3-26 sharpening and smoothing images 3-26 inverting images 3-27 embossing an image 3-27 flipping an image 3-27 cropping an image 3-28 placing annotations on an image 3-30 annotate toolbar 3-30 showing and hiding annotations 3-30 selecting the default color and line style for annotations 3-31 drawing a line 3-31 drawing a rectangle 3-32 drawing an ellipse 3-33 drawing a freehand shape 3-35 placing text on an image 3-39 drawing an arrow 3-41 changing annotations 3-43 exporting images and engraving saving and merging annotations 3-46 contents-2 imagesci and imagesource user manual[close]
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contents the imagesource application window 4 status bar 4-2 image capture toolbox 4-3 docking and floating the image capture toolbox 4-4 drawer icon 4-4 freeze/go live/snap image 4-5 open drawer 4-6 exposure time 4-6 automatic exposure 4-7 image series 4-7 lighting control 4-7 extended dynamic range edr control 4-8 neutral field correction nf control 4-9 image windows 4-9 zooming and scrolling image windows 4-10 image controls 4-13 three-dimensional view 4-14 original and processed view modes 4-15 the histogram window 4-16 showing and hiding the histogram window 4-16 docking and floating the histogram window 4-17 using the histogram window 4-18 histogram window cursors 4-19 browser 4-20 toolbars displaying and hiding arranging toolbars image sharpen smooth speckle correction invert flip horizontal flip vertical define region crop to region toolbars 5 5-1 5-2 5-2 5-2 5-2 5-2 5-3 5-3 5-3 5-3 5-3 imagesci and imagesource user manual contents-3[close]
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contents annotate select draw line draw rectangle draw ellipse draw freehand shape draw text draw arrow hollow/filled shapes color line style zoom zoom in zoom out zoom 1:1 zoom to fit standard new open save print image capture toolbox annotation toolbars image toolbar send to imageaide show histogram window 3d view context-sensitive help configuration 5-4 5-4 5-4 5-4 5-5 5-5 5-5 5-5 5-5 5-6 5-6 5-6 5-6 5-6 5-7 5-7 5-7 5-7 5-7 5-7 5-8 5-8 5-8 5-8 5-8 5-9 5-9 5-9 5-9 menus file menu new image from camera new image from file open image browse save image 6 6-1 6-1 6-2 6-3 6-4 6-5 contents-4 imagesci and imagesource user manual[close]
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contents save image as 6-5 close image 6-6 export image 6-7 merge annotation 6-8 create new composite image multiplexing 6-9 printer setup 6-12 report settings 6-13 print preview 6-13 print 6-14 most recently used files 6-15 exit 6-15 edit 6-16 cut 6-16 copy 6-16 paste 6-16 undo 6-16 view 6-17 annotation 6-17 histogram 6-18 grid on live 6-18 normal 1:1 6-18 zoom in 6-18 zoom out 6-19 view original 6-19 view processed 6-19 properties 6-20 status bar 6-23 3d view 6-24 window 6-24 cascade 6-24 tile horizontal 6-24 tile vertical 6-24 arrange icons 6-25 close all 6-25 windows open in imagesource 6-25 tools 6-25 image 6-26 annotate 6-26 imagesci and imagesource user manual contents-5[close]
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contents zoom standard extras user name report titles initial acquire state save configuration delete configuration promote configuration autoscale on capture image sharpen smooth invert flip horizontal flip vertical emboss define region of interest crop to region help contents index using help show wizard change wizard about imagesource 6-26 6-27 6-27 6-27 6-28 6-29 6-30 6-31 6-31 6-33 6-33 6-33 6-34 6-35 6-35 6-35 6-36 6-37 6-38 6-38 6-38 6-39 6-39 6-39 6-39 6-40 contents-6 imagesci and imagesource user manual[close]
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introduction and initial setup introduction this manual gives full instructions for setting up and using imagesci and for using the imagesource software the manual is divided into three parts introduction and initial setup this chapter getting started and reference the next section in this chapter gives a brief overview of the imagesci hardware and instructions for connecting up its components the final section of the chapter gives an overview of the software the getting started part of the manual takes you through basic procedures for capturing an image and sending it to imageaide for analysis the first chapter in the reference part of the manual chapter 3 using imagesource describes how to use setting configurations capture images and control the way images are displayed it then shows you how to work with captured images for presentation purposes including how to enhance them using a variety of techniques and how to add annotations chapter 4 the imagesource application window describes the layout of the program interface and shows you how to work with the image capture toolbox image windows the histogram window and the browser chapter 5 the toolbars describes some general features of working with toolbars and then provides instructions for using each of the tools chapter 6 menus describes each of the menus in turn with instructions for using the commands they contain imagesci and imagesource user manual 1-1[close]
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introduction and initial setup imagesci overview imagesci is an affordable fully-automated gel documentation and analysis system it features 16 bit performance with many outstanding features usually only associated with advanced systems standard imagesci systems are supplied with imagesci darkroom fitted with 8-bit 16-bit performance provided by edr ccd camera and prefocused f1.2 lens with standard uv filter integral transilluminator 15 x 15cm 302nm sample size 15 x 12cm uv/white light converter for white light applications optional built-in pc running windows xp 250mb internal zip and 1.44mb floppy drive imagesource acquisition software imageaide match analysis software microsoft office small business edition optional imagesci is supplied with all necessary software installed in the pc so all you need to do is to connect a keyboard mouse and monitor connecting up the system to connect up imagesci 1 unscrew the knurled fixing screw holding the cover plate on the left-hand side of the imagesci system box remove the cover plate to reveal the connectors beneath plug in the monitor keyboard and mouse leads the sockets are labelled with appropriate icons 2 3 note you should also connect any other accessories such as a printer to the appropriate connectors beneath the cover panel 1-2 imagesci and imagesource user manual[close]
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software overview 4 refit the cover panel slotting the cables through the cutouts and replace the knurled fixing screw to hold it in place connect power cables to the power sockets on the imagesci on the back and monitor 5 see getting started with imagesci chapter 2 for how to switch on the imagesci and use it to capture images software overview this section gives an overview of the software supplied with imagesci imagesource you use the imagesource program to control the hardware to capture images and to process the captured images in particular you can use imagesource to control the illumination and exposure length while viewing a live image from the camera you can use imagesource to capture images from a live image as a single frame capture in a series with the same or variable exposures using auto exposure the patented extended dynamic range edr feature allows you to extend the dynamic range of the system s camera in particular it increases the detail in low intensity areas of the image allowing you and analysis software like imageaide to distinguish features in dark parts of the object that would otherwise be undetectable without saturating the lighter areas the neutral field correction provided by imagesource allows you to correct for uneven illumination while maintaining good laboratory practice a histogram display allows you to maximize the image contrast without losing any detail for presentation purposes you can process captured images to create a negative image and increase or decrease the sharpness you can also crop images or flip them horizontally or vertically imagesource also allows you to add graphical and textual imagesci and imagesource user manual 1-3[close]
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introduction and initial setup annotations you can save the annotations in a separate file from the image to transfer them to other images all processing is performed on a copy of the original image which is saved with the original image in accordance with good laboratory practice imageaide always analyses the original unprocessed image in the image file original and processed images can be exported to files using a wide range of standard graphics formats and you can choose whether or not to `engrave the annotations on the exported image imageaide imageaide is an extremely powerful and easy-to-use gel analysis program it is fully automated allowing analyses to be carried out in seconds however it is also extremely flexible giving you the option to control every aspect of the analysis manually if you wish see the separate imageaide documentation for details summary your imagesci system should now be fully assembled and ready for use you should now go to the getting started chapter to find out how to turn it on and start working productively with it the first chapter in the reference part of the manual using imagesource builds on the getting started chapters and goes into rather more depth showing you alternative ways of proceeding and more advanced features the remaining chapters in the reference part of the manual provide a systematic reference to the imagesource software 1-4 imagesci and imagesource user manual[close]
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getting started with imagesci this chapter gives a quick introduction to using your imagesci system taking you through the processes of starting up capturing an image and opening the image in imageaide for analysis the final section of the chapter gives some hints on using imagesci there are other ways to carry out the operations described in this chapter providing powerful and time-saving alternatives for full details of these and the many other features offered by imagesource see using imagesource chapter 3 and the other reference chapters following it switching on to switch on the imagesci 1 2 make sure the power leads are connected to a live supply turn on the main imagesci power switch this is a rocker switch just above the power input socket on the back of the imagesci press the processor on/off button for a couple of seconds looking at the back of the imagesci this is a black push button switch at the top right-hand corner of the back panel turn on the monitor 3 4 the imagesci will take a little time to start up while it loads windows and then imagesource imagesci and imagesource user manual 2-1[close]
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getting started with imagesci when imagesource starts up the first time you will be asked to log on 1 type in your name if you have opened imagesource before and entered your name you will be able to select it from the drop-down list press ok to open imagesource 2 the main imagesource application window see chapter 4 will open with the image capture toolbox displayed on its left-hand side 2-2 imagesci and imagesource user manual[close]
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capturing an image from the camera capturing an image from the camera this section shows you how to carry out some typical procedures for capturing images you will learn how to capture an image using an automatic exposure see page 2-4 capture an image from live video see page 2-5 capture a single image with a long exposure see page 2-7 capture a series of images see page 2-8 capture an image with extended dynamic range see page 2-11 note you can apply neutral field correction with the first three of these methods but not in combination with edr see using neutral field correction nf page 3-11 for details once you have understood these examples you will be able to choose and if necessary modify the technique that best suits your own requirements and the samples you are using whichever technique you use the first task is to insert the sample since this procedure is common to all the capture techniques it is described before the separate procedures inserting the sample to insert the sample 1 2 prepare the sample if you have just switched on the imagesci the sample drawer at the bottom of the imagesci will be unlatched and you should open it by pulling it towards you note keep hold of the drawer and pull carefully to avoid pulling the drawer completely out of the imagesci if the sample drawer is closed this will be shown on the graphic in the image capture toolbox imagesci and imagesource user manual 2-3[close]
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getting started with imagesci and the open drawer button will be enabled press open drawer button to release the drawer and then open it by pulling it towards you see note above note if you have purchased the optional white light converter drawer and you want to capture an image using transmitted white light make sure it is fitted in place of the normal drawer 3 place the sample in the drawer and push it closed until it is latched by the magnetic catch the buttons in the image capture toolbox will become enabled if you want the wells to appear at the top of the image place the gel in the drawer with the well line on the left-hand side it is not essential to have the wells at the top of the image since imageaide will analyze gels in any orientation however gel images are normally shown with this orientation so it is usually convenient to maintain this convention 4 choose the gel sample configuration from the drop-down list box in the configuration bar at the top of the imagesource window note this is one of the system default configurations supplied with imagesource see working with configurations page 3-1 to learn more about using configurations the system is now ready to capture an image using one of the techniques in the following sections capturing an image using automatic exposure to carry out an image capture using an automatic exposure 1 follow the procedure in inserting the sample see page 2-3 to prepare the system for capturing an image 2-4 imagesci and imagesource user manual[close]
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capturing an image from the camera 2 press the automatic exposure button in the image capture toolbox note note you can press the automatic exposure button when the image is live or frozen these instructions have shown you how to capture an image using the settings saved in the gel sample configuration if you want to use other settings you can choose a different configuration or change the settings or options manually before carrying out step 2 imagesource determines the correct exposure by grabbing a series of images starting with the minimum exposure and then with increasing exposures until an image is grabbed that has some saturated areas the exposure is then reduced by one step and the image captured and displayed in an image window ready for further processing annotation or analysis as required the uv light inside the darkroom will be switched off automatically after the final exposure and the sample drawer will be released so that you can replace the sample capturing an image from live video to capture an image manually from live video 1 follow the procedure in inserting the sample see page 2-3 to prepare the system for capturing an image if a live image is not currently displayed press the green freeze/go live/snap image button in the image capture toolbox to display a live image in an image window provided the drawer is closed the lighting control will show that the uv illumination has come on 2 if no light is selected in the lighting control select transilluminator to turn the uv illumination on imagesci and imagesource user manual 2-5[close]
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getting started with imagesci 3 to set the exposure time a select the value hours minutes seconds or milliseconds that you want to change by clicking in it or by clicking on the scroll arrows at the right-hand end of the control b type the new value over the numbers or click on the up or down spin arrow at the left-hand end of the control to increase or decrease the number note you can also increase or decrease the exposure time by pressing the up or down arrow keys on the keyboard or if you are using a wheel mouse by turning the wheel as you increase or decrease the exposure time the live image will become lighter or darker adjust the exposure time to get a reasonably bright image of the gel without saturating any part of it note only certain values of exposure time are allowed if you type a non-allowed value directly into the box it will be corrected to the next allowed value 4 press the red freeze/go live/snap image button in the image capture toolbox the image will be captured frozen in the image window ready for further processing annotation or analysis as required the uv light inside the darkroom will be switched off automatically after the exposure and the sample drawer will be released so that you can remove the sample 2-6 imagesci and imagesource user manual[close]
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capturing an image from the camera capturing a single image with an exposure longer than five seconds to capture a single image with a long exposure note because it can be difficult to estimate the best exposure setting in advance if the exposure is long imagesource also allows you to capture a series of images with different exposures so that you can choose the best one after the images have been captured see the next section for details 1 follow the procedure in inserting the sample see page 2-3 to prepare the system for capturing an image if the image is live press the red freeze/go live/snap image button in the image capture toolbox to freeze the image the button will turn green 2 note you cannot set the exposure to more than 5 seconds when the image is live 3 to adjust the exposure time note the freeze/go live/snap image button turns blue when the exposure is set longer than 5 seconds a select the value hours minutes seconds or milliseconds that you want to change by clicking in it or by clicking on the scroll arrows at the right-hand end of the control b type the new value over the numbers or click on the up or down spin arrow at the left-hand end of the control to increase or decrease the number note you can also increase or decrease the exposure time by pressing the up or down arrow keys on the keyboard or if you are using a wheel mouse by turning the wheel imagesci and imagesource user manual 2-7[close]
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getting started with imagesci note only certain values of exposure time are allowed if you type a non-allowed value directly into the box it will be corrected to the next allowed value the values allowed depend on the system you are using 4 press the blue freeze/go live/snap image button in the image capture toolbox to capture the image the button will turn gray while the image is captured the captured image will be shown in a new image window capturing a series of images to capture a series of images from a sample 1 follow the procedure in inserting the sample see page 2-3 to prepare the system for capturing an image press the image series button in the image capture toolbox to display the series capture dialog box 2 3 set the number of images you want to capture in the series by clicking on the arrow buttons next to the number of images in series spin box you can choose from 1 to 100 inclusive check add contents of previous images to each new image if you want the results to be cumulative each new image is the result of adding the new exposure to the previous image in the series 4 2-8 imagesci and imagesource user manual[close]
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capturing an image from the camera uncheck add contents of previous images to each new image if you want all images in the series captured with the set exposure 5 check use same exposure for all images in series if you want to set a single exposure for all images go to step 5 note if you check both use same exposure for all images in series and add contents of previous images to each new image the exposure time for the first image will be the set exposure for the second image the effective exposure time will be 2× the set exposure for the third it will be 3× the set exposure and so on uncheck use same exposure for all images in series if you want to set a separate exposure for each of the images go to step 6 6 if you have checked use same exposure for all images in series you can adjust the exposure time as follows a select the value hours minutes seconds or milliseconds that you want to change by clicking in the exposure time control or by clicking on the scroll arrows at the right-hand end of the control b type the new value over the numbers or click on the up or down spin arrow at the left-hand end of the control to increase or decrease the number note you can also increase or decrease the exposure time by pressing the up or down arrow keys on the keyboard or if you are using a wheel mouse by turning the wheel only certain values of exposure time are allowed if you type a non-allowed value directly into the box it will be corrected to the next allowed value note imagesci and imagesource user manual 2-9[close]
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