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imageaide reference although all possible care has been taken in the preparation of this publication 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 © synoptics limited 20002004[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 using imageaide for gel analysis 1 how to create and work with secure sample files 1-1 file formats 1-1 opening a secure sample file 1-2 creating a new secure sample file 1-10 using the browser 1-11 acquiring an image to create a secure sample file 1-13 importing settings from existing secure gel sample files 1-14 editing sample properties 1-20 saving a secure sample file 1-20 how to place position and work with tracks 1-21 overview 1-21 locating tracks automatically 1-23 locking tracks 1-24 placing individual tracks on a sample 1-25 deleting tracks 1-29 adjusting the overall position of the tracks on a sample 1-29 adjusting the track splay 1-31 moving and tilting a single track 1-33 adjusting track width 1-39 adjusting the rf start and end lines 1-41 enabling and disabling tracks 1-45 adding a description for a track 1-46 displaying track properties 1-47 how to set the background correction for tracks 1-50 setting the integration parameters 1-50 setting or changing a manual baseline 1-55 deleting a manual baseline 1-58 how to locate and edit peaks on a track 1-58 locating the peaks on a track automatically 1-59 imageaide user manual contents-1[close]
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contents adding a peak semi-automatically 1-60 adding a peak manually 1-62 selecting peaks 1-63 deleting peaks 1-66 adjusting the position of a peak 1-67 adjusting the position of a peak s bounds 1-69 displaying peak properties 1-70 how to create molecular weight calibrations 1-71 assigning molecular weights to a standard track 1-71 specifying how molecular weights are calculated from standard tracks 1-77 removing molecular weight assignments from peaks 1-79 reassigning molecular weights in a standard track 1-80 molecular weight configuration settings 1-82 the molecular weight calibration graph 1-83 viewing molecular weights calculated from the tracks 1-83 working with molecular weight libraries 1-85 how to create quantity calibrations 1-96 setting the quantity calibration method 1-97 assigning quantities to peaks 1-99 the quantity calibration graph 1-100 viewing quantities calculated from the tracks 1-101 how to compare peak profiles 1-102 changing the scale in the profile comparison window 1-106 printing reports profile comparisons 1-106 how to match peaks on different tracks 1-107 setting the tolerance and method used for peak matching 1-107 setting a matching standard 1-108 editing matches 1-109 viewing match results 1-110 dendrogram 1-113 how to print and export gel results 1-115 printing a report showing gel results 1-115 exporting results to excel 1-117 saving results in a comma separated values format file 1-118 creating a report in word 1-119 copying a picture of an image to the clipboard 1-120 contents-2 imageaide user manual[close]
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contents using imageaide for manual band quantification using imageaide for spot blot analysis 2 3 how to create and work with secure sample files 3-1 opening a secure sample file 3-2 creating a new secure sample file 3-6 using the browser 3-7 acquiring an image to create a secure sample file 3-9 importing settings from existing secure spot blot sample files 3-10 importing settings from a saved sample file 3-15 editing sample properties 3-16 saving a secure sample file 3-16 how to add and remove spot frames 3-17 adding spot frames automatically 3-17 adding new spot frames 3-18 removing spot frames 3-21 how to adjust the size and shape of spot frames 3-22 setting the size of all spot frames to the same size and shape 3-22 changing between circular and rectangular spot frames 3-22 adjusting the size of circular spot frames 3-23 adjusting the size and shape of rectangular spot frames 3-25 how to adjust the spot frame positions 3-26 adjusting the position of a single spot frame 3-26 adjusting the positions of all the spot frames in a grid 3-27 how to lock the spot frames on a sample 3-32 how to show or hide identification labels on the spot frames 3-33 how to set the quantity calibration method 3-33 how to assign quantities to spot frames 3-34 how to apply background correction to results 3-36 how to view spot blot results 3-38 how to define an incidence condition 3-39 how to print and export spot blot results 3-41 printing spot blot results 3-41 exporting spot blot results to excel 3-42 saving results in a comma separated values format file 3-43 copying a picture of an image to the clipboard 3-44 imageaide user manual contents-3[close]
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contents using imageaide to count colonies windows 4 5 gel windows 5-2 adjusting the panes in a gel window 5-3 track label pane 5-3 description pane 5-4 image pane 5-4 profile pane 5-6 peak value pane 5-6 graphics pane 5-7 results pane 5-13 molecular weight library window 5-15 profile comparison window 5-16 colony counting window 5-20 spot blot/manual band quantification window 5-22 image pane 5-23 results/incidence/calibration graph pane 5-25 image controls 5-27 the histogram viewer 5-28 toolbars the standard toolbar open save help sample properties report toolbar report setup preview print export table to excel save table to csv file export to word save to clipboard track toolbar locate tracks 6 6-1 6-1 6-1 6-2 6-2 6-2 6-2 6-2 6-3 6-3 6-3 6-3 6-3 6-4 6-4 contents-4 imageaide user manual[close]
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contents lock all 6-4 position all 6-4 splay all 6-5 move/tilt 6-5 width 6-5 rf start position 6-5 rf end position 6-5 zoom toolbar 6-6 zoom in 6-6 zoom out 6-6 zoom reset 6-6 calibrations toolbar 6-6 integration parameters 6-7 quantity calibration 6-7 assign quantity 6-7 molecular weight calibration 6-7 mw standard 6-7 profile comparison window 6-8 peak matching toolbar 6-8 peak matching 6-8 matching standard 6-8 spot blot toolbar 6-9 all spots same size 6-9 position control points 6-9 locate 6-9 position any spot 6-9 background correction 6-10 lock position 6-10 spot incidence parameters 6-10 circle 6-10 rectangle 6-11 free hand 6-11 quantity calibration parameters 6-11 assign quantity 6-11 menus 7 file sample window 7-1 imageaide user manual contents-5[close]
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contents new import 7-2 open 7-7 browse 7-9 close 7-10 save 7-10 save as 7-11 select source twain 7-12 acquire twain 7-12 new library 7-13 open library 7-14 import method 7-14 export table to excel 7-16 save table to csv file 7-17 export to word 7-18 save to clipboard 7-19 printer setup 7-19 report setup 7-20 print preview 7-26 print 7-27 recently opened files 7-28 sample properties 7-28 exit 7-37 file molecular weight library window 7-38 unlock 7-38 lock 7-39 change password 7-40 properties 7-41 edit gel window 7-42 integration parameters 7-42 molecular weight calibration 7-48 quantity calibration 7-50 peak matching 7-52 edit spot blot/manual band quantification window 7-53 quantity calibration 7-53 edit colony counting window 7-54 edit molecular weight library window 7-54 new standard 7-54 edit standard 7-56 contents-6 imageaide user manual[close]
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contents delete standard rename standard edit profile comparison window view gel window profile comparison histogram zoom in zoom out zoom reset align banks of tracks display corrected profiles peak markers peak bounds tracks match lines peak numbers only molecular weight quantities peak matching maximize pane toolbars submenu toolbar buttons on menus status bar view spot blot/manual band quantification window spot numbers view colony counting window view profile comparison window view molecular weight library window track locate tracks width individual height individual lock all position all splay all move/tilt width rf start position 7-57 7-58 7-59 7-59 7-60 7-60 7-60 7-60 7-61 7-61 7-61 7-61 7-62 7-62 7-62 7-62 7-63 7-63 7-63 7-63 7-64 7-64 7-64 7-65 7-65 7-66 7-66 7-66 7-67 7-67 7-68 7-68 7-68 7-69 7-71 7-73 7-78 7-80 imageaide user manual contents-7[close]
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contents rf end position 7-80 invert profile 7-84 edit manual baseline 7-84 delete manual baseline 7-88 mw standard 7-88 matching standard 7-89 insert 7-90 delete 7-93 enable 7-93 disable 7-94 description 7-94 properties 7-95 peak 7-97 assign molecular weight 7-97 assign quantity 7-103 unassign molecular weight 7-105 unassign quantity 7-105 locate submenu 7-106 delete submenu 7-106 match submenu 7-107 properties 7-107 profile 7-108 reference 7-108 show 7-108 properties 7-109 spots 7-109 circle 7-110 rectangle 7-110 free hand 7-110 all spots same size 7-112 position control points 7-112 locate 7-113 position any spot 7-114 background correction 7-115 lock position 7-115 spot incidence parameters 7-116 delete 7-117 delete all 7-118 contents-8 imageaide user manual[close]
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contents assign quantity unassign quantity extras user name configuration save sample defaults load sample defaults window new window cascade tile arrange icons windows open in imageaide help help topics using help about imageaide image pane and profile context menus track label context menu active matching standard peak value pane context menu delete graphics pane context menu scale to fit save to clipboard gel window results pane context menu result table commands profile comparison window context menu spot blot/manual band quantification window spot blot/manual band quantification window result table commands table 1d/table 2d molecular weight library context menu image pane context menu results pane context menu 7-118 7-120 7-120 7-121 7-121 7-128 7-129 7-129 7-129 7-129 7-130 7-130 7-130 7-130 7-130 7-130 7-131 7-131 7-131 7-132 7-132 7-132 7-133 7-133 7-133 7-134 7-134 7-135 7-135 7-136 7-136 7-137 7-137 imageaide user manual contents-9[close]
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using imageaide for gel analysis this chapter contains detailed instructions for using imageaide for gel analysis it begins by describing how you can load sample files and images into imageaide it then shows you how to detect place and edit tracks on the image and then detect place and edit peaks on the tracks this is followed by instructions for calibrating the molecular weights represented by the peaks on a standard track including how you can use libraries of molecular weight standards there is then a section showing you how to calibrate the tracks so that you can measure quantities from the gel the chapter continues by showing you how to display a window comparing the profiles on different tracks including how to compare the profiles of tracks on different gels the next section describes how to use imageaide to match the peaks on different tracks to a standard track the final section in the chapter tells you how to print and export result reports how to create and work with secure sample files file formats imageaide stores data in a secure file format an .sgd file these files are also created by compatible acquisition programs such as imagesource the secure file format ensures that your data cannot be tampered with and that your results are both traceable and reproducible in keeping with good laboratory practice secure sample files may be analyzed files that have been previously saved in imageaide these will contain for a gel information about track positions peaks assigned standards results for molecular weights quantities and peak matching and so on imageaide user manual 1-1[close]
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using imageaide for gel analysis unanalyzed files that have been saved in an acquisition program but have not yet been loaded into and saved in imageaide opening a secure sample file below shows you how to open both unanalyzed and analyzed secure sample files however you can also load other image files created by non-secure sources such as tiff images generated by a scanner into imageaide for analysis when you do this imageaide copies the original image and saves it in a secure file any changes you then make to the original image will have no effect on the image in the secure file full details are given in creating a new secure sample file page 1-10 opening a secure sample file to open a secure sample file 1 choose open from the file menu to display a standard windows open dialog box 2 use the dialog box to select the required secure sample file 3 press open 1-2 imageaide user manual[close]
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how to create and work with secure sample files what happens next depends on whether you are opening an analyzed or unanalyzed secure sample and in the latter case on whether you have set auto import methods in the imageaide configuration dialog box if you are opening an analyzed secure sample file the sample will be opened in a gel window with all tracks and peaks displayed as they were when the file was last saved all previously analyzed results will be shown in the results tables if you are opening an unanalyzed secure sample file and you have selected auto import methods in the imageaide configuration dialog box the import method dialog box will open so that you can choose which settings to import see opening or creating a secure sample file with automatic import page 1-15 for further details if you are opening an unanalyzed secure sample file with auto import methods deselected the sample properties dialog box will open with the image loaded imageaide user manual 1-3[close]
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