NIS-Elements AR

245 Pages·2015·5.26 MB·English

M378E
15.10.NF.25

*M378EN25*

NIS-Elements AR
(Advanced Research)

User’s Guide
(Ver. 4.50)

Thank you very much for choosing Nikon.
This manual explains installation and use of the NIS-Elements Advanced Research. For
trouble-free operation, read this manual before using the program.

No part of this manual may be reproduced and transmitted without Nikon’s permission.
The content of this manual is subject to change without notice.
Nikon has carefully prepared this manual. However, we make no expressed or implied
warranty of any kind and assume no responsibility for such errors or omissions.
Be sure to read the instruction manuals for the microscope and PC you plan to use with the
NIS-Elements Advanced Research.

Trademarks:
Microsoft® and Windows® are either registered trademarks or trademarks of Microsoft
Corporation in the United States or other countries.
Products and brand names are trademarks or registered trademarks of their respective
companies.
The “TM” and ®marks are not used to identify registered trademarks and trademarks in this
manual.

To run NIS-Elements Advanced Research optimally, the following specifications are required.
Minimum PC Specification:
CPU: Intel Core 2 Duo or higher
RAM for 32bit OS: 2GB or higher
RAM for 64bit OS: 4GB or higher
Operating system: Windows 7 Professional SP1 64bit (English)
HDD: 2GB or more of available hard disk space for installation
Display: 1280x1024 pixel (True Color mode)
User rights: Administrators for installation
* Operation cannot be guaranteed on all computer models. For further information, contact
your nearest Nikon representatives.

NIS-ElementsAR
Table of Contents
1.CommandLineStartupOptions........................................................................................... 1
2.InstallationandSettings..................................................................................................... 5
2.1.InstallationandUpdates.......................................................................................... 5
2.2.AdditionalModulesAvailableinNIS-ElementsAR ..................................................... 12
2.3.UserRights.......................................................................................................... 14
2.4.NIS-ElementsPreferences...................................................................................... 21
2.5.NIS-ElementsERPackage...................................................................................... 23
3. UserInterface ................................................................................................................. 25
3.1.MainWindowComponents..................................................................................... 25
3.2.ImageWindow...................................................................................................... 28
3.3.ArrangingUserInterface........................................................................................ 31
3.4. Layouts ............................................................................................................... 32
3.5.LayoutManager.................................................................................................... 33
3.6.ModifyingToolbars................................................................................................ 34
3.7.ModifyingMenus................................................................................................... 36
3.8.RunningaMacroUponLayoutChange..................................................................... 37
3.9.AppearanceOptions.............................................................................................. 37
4.Cameras&Devices.......................................................................................................... 41
4.1.BasicWorkflows.................................................................................................... 41
5. Image Acquisition............................................................................................................ 63
5.1.IntroductiontoImageAcquisition............................................................................ 63
5.2. Shading Correction ............................................................................................... 64
5.3. Camera ROI ......................................................................................................... 65
5.4.AboutNDAcquisition............................................................................................. 67
5.5.Time-lapseAcquisition........................................................................................... 69
5.6.Multi-pointAcquisition........................................................................................... 73
5.7.Z-seriesAcquisition................................................................................................ 77
5.8.Multi-channelAcquisition....................................................................................... 79
5.9.Large-imageAcquisition......................................................................................... 81
5.10. Inputs/Outputs Control ........................................................................................ 82
5.11.CombinedNDAcquisition..................................................................................... 83
5.12.CapturingtoRingBuffer....................................................................................... 87
6.DisplayingImages............................................................................................................ 89
6.1.Open,Save,CloseImages...................................................................................... 89
6.2.ImageLayers........................................................................................................ 95
6.3.NDDimensions................................................................................................... 100
6.4. Large Images ..................................................................................................... 123
6.5.LUTs-Non-destructiveImageEnhancement........................................................... 125
6.6.Organizer........................................................................................................... 134
7.ImageAnalysis............................................................................................................... 139
7.1. Preparation ........................................................................................................ 139
7.2. Image Segmentation ........................................................................................... 143
7.3.BinaryLayers...................................................................................................... 149
7.4.RegionsofInterest-ROIs..................................................................................... 157
8. Measurement ............................................................................................................... 163
8.1.BasicWorkflows.................................................................................................. 163
8.2. ManualMeasurement......................................................................................... 179
8.3.AutomatedMeasurement..................................................................................... 184
8.4.TimeMeasurement............................................................................................. 186
8.5. Measurement Features ....................................................................................... 191
9. Creating Reports ........................................................................................................... 213
9.1.ReportGenerator................................................................................................ 213
9.2. Report Objects ................................................................................................... 214
9.3.ReportTemplates................................................................................................ 215
10.Macros....................................................................................................................... 217
10.1.CreatingMacros................................................................................................ 217
10.2.RunningaMacro............................................................................................... 219
10.3.MacroLanguageSyntax..................................................................................... 219
10.4.ControllingCamerasbyMacro............................................................................ 227
10.5.MacroPreferences............................................................................................ 227
11. Movies ....................................................................................................................... 229
11.1.CapturingAVIMovie........................................................................................... 229
11.2.SaveND2asAVI............................................................................................... 229
11.3.CreatingaMovie............................................................................................... 230
11.4. About Video Compression .................................................................................. 231
General Index ................................................................................................................... 233
CommandLineStartupOptions
1. Command Line Startup Options
Seealso2.1.3.CommandLineInstallationOptions.
WhenstartingNIS-Elementsfromthecommandline(orwheneditingthedesktopshortcutproperties),
youmayappendsomeswitcheswithparameterstothemaincommandandtherebymodifythestartup
behavior.
Note
Someswitchesdonothaveparameters.
Example1.1.Commandlineswitchessyntax
“NIS-Elementsexecutable”switch#1parameter#1switch#2parameter#2etc.
Forexample,torunNIS-ElementsARandopenthestarting_image.jp2atstraightaway,run.:
"c:\Program Files\NIS-Elements\nis_ar.exe" -f "C:\Images\starting_im-
age.jp2"
StartupSwitches
-?Displaysahelpscreenwiththedescriptionofswitches(basicallythispage).
-c“Command” TheapplicationrunsthespecifiedmacroCommand.
-cam“CameraName” ThespecifiedCamerawillbeused.Whenusingthisoptionyoumustalsospecify
theGrabberNameandtheHWUnitName.Tofindthecameraname,searchtheapplicationlogfilefor
“CameraName”.ItisalsopossibletouseonlyapartoftheCameraName,butthepartofthename
mustbeuniqueamongalltheavailablecameras.
-cw“CommandWait” Theapplicationrunsthespecifiedmacrocommandandwaitsuntilitiscompleted
-f“Filename” TheapplicationtriestoopentheimagepointedtobytheFilenameparameter.
-g“GrabberName” Theimagegrabber(driver)ofthespecifiedGrabberNamewillbeusedandno
camera-selectionwindowwillshowatstartup.Settheparametervalueto“last”andthemostrecently
usedgrabber/camerawillbeloaded.Asthegrabbername,youmustuseinternalnameofthegrabber,
nottheoneyouseeinthestartupdialogwindow.
Eitheruseoneofthefollowingnamesorsearchtheapplicationlogfileforthephrase“GrabberName”
(seeFixedGrabberStartup).
-gnNograbber(camera)driverwillbeloaded.Imageacquisitionwillnotbepossible.
-h“HWUnitName” ThespecifiedHWUnitwillbeused.Whenusingthisoptionyoumustalsospecify
theGrabberName.TwoHWUnits(e.g.twoDS-U2cameras)canberunbyonegrabber/driver.The
availableHWUnitsarelistedinthe Acquire>Select*cameraname* window.Settheparameter
valueto“select”andtheselectionboxwillbeshown.Whenusingthisoptionyoumustalsousethe-g
switch.TofindtheHWUnitName,pleasesearchthroughtheapplicationlogfilefor“HWUnitName”.
-i“ConfigName” AusercanspecifytheconfigurationtobeusedbyNIS-Elements.Thedefaultconfig-
urationissavedinthe“C:\ProgramData\LaboratoryImaging\Platform”folder.Ifyouwanttocreatea
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customconfiguration,usethe-iswitch,e.g.:nis_ar.exe -i "My_Configuration".Theconfig-
urationofthisinstancewillbesavedtothe"C:\ProgramData\Laboratory Imaging\My_Con-
figuration"folder.
Thisisusefulwhenusingtwocamerasononemicroscopeforexample.Youcancreateaseparatepro-
gramshortcutwhichusesthe-iswitchtoloadadifferentconfiguration.
-l“Language” Theapplicationwillruninthespecifiedlanguage(ifavailable).Usethree-letterlanguage
codesaccordingtotheISO639[http://en.wikipedia.org/wiki/List_of_ISO_639-2_codes]standard.
-m“MacroFile” Theapplicationwillexecutethemacrofile(*.mac)pointedtobytheMacroFilepara-
meter.
-mw“MacroFile” Theapplicationwillexecutethemacrofile(*.mac)pointedtobytheMacroFile
parameterandwaituntilitiscompleted.
-p“Command”[“Param”]TheapplicationwindowwillbeplacedaccordingtotheCommand.Possible
valuesare:
• left,right,top,bottom-thewindowisplacedonthecorrespondingmonitorscreen.
• monitorN-thewindowisplacedontheNthmonitor.
• rectangle(x0,y0,x1,y1)-thewindowisplacedinthespecifiedrectangle(inworkspacecoordinates).
Thecoordinatesmustbeinparenthesiswithoutanyspaces.
-passiveTheapplicationwillnotconnecttoanydeviceonstartup(NIS-ElementsARwillstartwithblank
DeviceManager).Cameraselectionisnotaffectedbythisoption.
-qAnewinstanceoftheapplicationwillrun.Bydefault,onlyoneinstanceofNIS-Elementsisallowed
torun.
-s“SettingsFile” TheapplicationwillusethespecifiedSettingsFiletoloadandsaveitssettings.The
settingsfilecanbecreatedfromMSWindowsStartmenubytheNISSettingsUtility.
-var,-vbr,-vd,-vfFortestingpurposes,youcanswitchtheapplicationtorunasifyouhaveadifferent
version(AR/BR/D/Freeware)installed.However,youhavetohavethecorrespondinglicencewrittenin
yourkey(EvenifyounormallyrunNIS-AR,the-vdswitchwillnotworktorunNIS-Dunlessyouhavealso
theNIS-Dlicence).
Note
Mindthatthesetoffunctionsyouwillgetoncethesoftwareisrundependsonthesetupfileused
forinstallation(forexample,somefunctionsofNIS-DarenotincludedintheNIS-ARsetupsothese
willnotappearinthesoftwarerunby:nis_ar.exe -vd
FixedGrabberStartup
EachtimeNIS-ElementsARisrunorthegrabber/camera/HWunitischanged,fourparametervalues
arewrittentotheapplicationlogfile(C:\ProgramData\LaboratoryImaging\Platform\Logfiles).:
• GrabberName
• HWUnitName
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CommandLineStartupOptions
• HWUnitConnectionString
• CameraName
Let'ssaywewanttosetthelastusedconfigurationforeveryNIS-ElementsARstart:
1. Lookuptheparametersinthemostrecentlogfile.E.g.:
GrabberNameCLxGrabberDriverSim
HWUnitNameSimGrabber
HWUnitConnectionString(empty)
CameraNameSim_Camera_Color
2. Modifytheshortcut,E.g.:
"c:\Program Files\NIS-Elements\nis_ar.exe" -g CLxGrabberDriverSim -h
SimGrabber -cam Sim_Camera_Color
3. Double-clicktheshortcut.NIS-Elementswillstartwithoutaskingforgrabberselection
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