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Image J user-guide_图文
导读：NoteworthyIIIIIIIVVVIVIIVIIIIXXXIXIIXIIIXIVXVXVIFrontmostWindowandWindowActivation.....................9ImageTypes:LossyCompressionandMetadata...................12OpeningVirtualSta
Noteworthy
XVIFrontmostWindowandWindowActivation.....................9ImageTypes:LossyCompressionandMetadata...................12OpeningVirtualStacksbyDrag&Drop.......................13ReplacingRedwithMagentainRGBImages....................16TogglingCalibratedUnits...............................29OpeningFilePathsintheLogWindow.......................46OrganizingCommandsintheMenuBar.......................48OpeningFiles:File??Open...,File??Import??andDrag&Drop...........50ReducingMemoryRequirementsWhenImportingImages.............53WarningonJPEGCompression............................57DrawingLinesWiderThanOneCPixel........................62TransferringSelectionsBetweenImages.......................64ConvertingCompositeSelections...........................66ApplyingAutoBrightness/ContrasttoEntireStacks................76DisplayRangeofDICOMImages...........................78Brightness/ContrastofHighBitCDepthImages...................79
XVIIEmbeddingColorAnnotationsinGrayscaleImages.................86XVIIIWorkingwithZoomedCanvases............................101XIX
XXIHexadecimalColorValues...............................103CreatingBinaryMasks.................................113SkeletonizevsSkeletonize3D..............................115XXIIInterpretingBinaryImages..............................118XXIIIGlobalCalibrations...................................141XXIVUsingScannersinDensitometry............................144XXVSelectingROIsintheROIManager..........................153XXVIFocusonBioimageInformatics............................173
MacroListings
11ReplaceRedwithMagenta.ijm(UsingProcess??ImageCalculator...)........17ReplaceRedwithMagenta.ijm(UsingImage??Color??Channels...).........17EnsuringSpeci?cSettingsatLaunch.........................22CustomizingtheImagePopupMenu.........................42CustomizingtheFloatBehaviorofIJ’sMainWindow...............47SettingFile??OpenSamples??forO?ineUsage....................51UsingaKeyboardShortcuttoChangeSelectionColor...............70ObtainingHistogramLists...............................142AssigningKeyboardShortcutstoImageJTools...................169CyclingThroughtheToolbarUsingKeyboardShortcuts..............170TemporaryActivationofaTool............................170
GuideFormats
Thisguideisavailableinthefollowingformats:
EnhancedPDFOptimizedforelectronicviewingandhighlyenrichedinhypertextlinks(seeConventionsUsedinthisGuide).Availableathttp://imagej.nih.gov/ij/docs/guide/user-guide.pdf.
HTMLdocumentavailableonlineathttp://imagej.nih.gov/ij/docs/guide/.Foro?ineus-ageadownloadableZIParchiveisalsoavailableathttp://imagej.nih.gov/ij/docs/user-guide.zip.
PrintablebookletsTwo-sidedbookletsthatcanbeprintedonaduplexunitprinterbysettingtheautomaticduplexmodeto“shortedgebinding”.Twoformatsareavailable:A4(http://imagej.nih.gov/ij/docs/guide/user-guide-A4booklet.pdf)andlettersizepaper(http://imagej.nih.gov/ij/docs/guide/user-guide-USbooklet.pdf).ConventionsUsedinthisGuide
Throughouttheguide,internallinksaredisplayedingray(e.g.,PartIVImageJUserInterface).LinkstoexternalURLs,suchastheImageJwebsite,http://imagej.nih.gov/ij/,aredisplayedindarkblue.
ImageJcommandsaretypedinsansseriftypefacewithrespectiveshortcutkeys?ankedbysquarebrackets(e.g.:Image??Duplicate...[D]).As
,thisnotationimpliesShift-modi?ers(i.e.,[D]meanspressing[d]onlythe
key)andassumesthatRequirekeyfor
Edit??isNote
keyofMacintoshkeyboards.thatreferencestothekeyincludethe
Usefultipsandremindersareplacedin‘Noteworthynotes’numberedwithuppercaseromannumerals(e.g.,IFrontmostWindowandWindowActivation).Thefulllistofthesenotesisavailableonpageviii.
Filenames,directoriesand?leextensionsaretypedinmonospacedfontmarkedbyarelatedicon,e.g.,?leStartupMacros.txtinfolder.
Macrofunctionsandcodesnippetsaretypedinmonospacedfont,e.g.,resetMinAndMax().Scriptsandmacrosarenumberedwitharabicnumeralsincludedinparentheses(e.g.,(2)ReplaceRedwithMagenta.ijm(UsingImage??Color??Channels...)onpage17)andtypesetwiththesamesyntaxmarkupprovidedbytheFijiScriptEditor.Thefulllistofmacrolistingsisavailableonpageix
Selectedhighlightsofversion1.46rarelistedonpageviiand?aggedwith
coloredmarginalnotes.Theseshouldbeinterpretedas:
AnewfeatureimplementedinImageJ1.46r.Aroutinethathasbeenimprovedsincepreviousversions.Typically,
afasterormoreprecisealgorithm,acommandwithbetterusability,orataskthathasbeenextendedtomoreimagetypes.Apre-existingcommandthathasbeenrenamedormovedtoadi?erentmenulocationinImageJ1.46r.
GettingStarted
ThispartprovidesbasicinformationonImageJinstallation,troubleshootingandupdatestrategies.ItdiscussesFijiandImageJ2aswellasthird-partysoftwarerelatedtoImageJ.BeingimpossibletodocumentallthecapabilitiesofImageJwithoutexploringtechnicalaspectsofimageprocessing,externalresourcesallowingwillingreaderstoknowmoreaboutdigitalsignalprocessingarealsoprovided.
1Introduction
ImageJisapublicdomainJavaimageprocessingandanalysisprograminspiredbyNIHImagefortheMacintosh.Itruns,eitherasanonlineappletorasadownloadableapplication,onanycomputerwithaJava1.5orlatervirtualmachine.DownloadabledistributionsareavailableforWindows,MacOSXandLinux.Itcandisplay,edit,analyze,process,saveandprint8Cbit,16Cbitand32Cbitimages.ItcanreadmanyimageformatsincludingTIFF,GIF,JPEG,BMP,DICOM,FITSand‘raw’.Itsupports‘stacks’(andhyperstacks),aseriesofimagesthatshareasinglewindow.Itismultithreaded,sotime-consumingoperationssuchasimage?lereadingcanbeperformedinparallelwithotheroperations1.
Itcancalculateareaandpixelvaluestatisticsofuser-de?nedselections.Itcanmeasuredistancesandangles.Itcancreatedensityhistogramsandlinepro?leplots.Itsupportsstandardimageprocessingfunctionssuchascontrastmanipulation,sharpening,smoothing,edgedetectionandmedian?ltering.
Itdoesgeometrictransformationssuchasscaling,rotationand?ips.Imagecanbezoomedupto32:1anddownto1:32.Allanalysisandprocessingfunctionsareavailableatanymagni?cationfactor.Theprogramsupportsanynumberofwindows(images)simultaneously,limitedonlybyavailablememory.
Spatialcalibrationisavailabletoproviderealworlddimensionalmeasurementsinunitssuchasmillimeters.Densityorgrayscalecalibrationisalsoavailable.
ImageJwasdesignedwithanopenarchitecturethatprovidesextensibilityviaJavaplugins.Customacquisition,analysisandprocessingpluginscanbedevelopedusingImageJ’sbuiltineditorandJavacompiler.User-writtenpluginsmakeitpossibletosolvealmostanyimageprocessingoranalysisproblem.
Beingpublicdomainopensourcesoftware,anImageJuserhasthefouressentialfreedomsde?nedbytheRichardStallmanin1986:1)Thefreedomtoruntheprogram,2)Thefreedomtostudyhowtheprogramworks,andchangeitt3)Thefreedomtoredistributecopiessoyo4)Thefreedomtoimprovetheprogram,andreleaseyourimprovementstothepublic,sothatthewholecommunitybene?ts.ImageJisbeingdevelopedonMacOSXusingitsbuiltineditorandJavacompiler,plustheBBEditeditorandtheAntbuildtool.Thesourcecodeisfreelyavailable.Theauthor,WayneRasband(wsr@nih.gov),isaSpecialVolunteerattheNationalInstituteofMentalHealth,Bethesda,Maryland,USA.
Seealso:HistoryofImageJatimagejdev.org
1AsomehowoutdatedlistofImageJ’sfeaturesisavailableathttp://imagej.nih.gov/ij/features.html
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You have full text access to this Open Access contentCPT: Pharmacometrics & Systems PharmacologyEdited By: Piet van der Graaf, PhD, PharmDOnline ISSN: Associated Title(s): ,
Editorial Board
Editor-in-Chief
Piet van der Graaf, PhD, PharmDDr. van der Graaf is
Professor of Systems Pharmacology and Chair of Pharmacology at
Leiden University (The Netherlands) and Vice President and Head of
Quantitative Systems Pharmacology (QSP) at Certara. Previously, he
was Director of Research at the Leiden Academic Centre for Drug
Research (LACDR). From 1999 & 2013 he held various leadership
positions at Pfizer in Sandwich (United Kingdom) in Discovery
Biology (Head of Sexual Health Therapeutic Area), Pharmacokinetics
and Drug Metabolism (Head of Translational Quantitative
Pharmacology) and Clinical Pharmacology/Pharmacometrics
(responsible for the Pain portfolio). He received his doctorate
training in quantitative receptor pharmacology with Nobel laureate
Sir James Black at King's College London and thereafter worked as a
postdoctoral fellow of the Royal Netherlands Academy of Sciences at
Leiden University on the development of mechanism-based
pharmacokinetic-pharmacodynamic (PKPD) approaches. He is Fellow of
the British Pharmacological Society, has (co-)authored more than
100 papers in the area of quantitative and translational
pharmacology, including the seminal 2011 NIH White Paper
&Quantitative and Systems Pharmacology in the Post-genomic Era: New
Approaches to Discovering Drugs and Understanding Therapeutic
Mechanisms&.
Deputy Editor-in-Chief
Lena Friberg, PhD
Dr. Friberg is a Professor in the Department of Pharmaceutical
Biosciences at Uppsala University in Sweden. She holds a Masters in
Pharmaceutical Sciences and a PhD from Uppsala University. Her
research focuses on pharmacometrics and development of population
pharmacokinetic and pharmacodynamic models for desired effects and
adverse events in a range of therapeutic areas, such as oncology,
bacterial infections, schizophrenia, rheumatoid arthritis, and QT
prolongation. Currently, most of her research is focused on
development of PKPD-models for quantitative, longitudinal
predictions of use for translation of drug effects from preclinical
(in vitro and in vivo) to patients and from early to late clinical
development.
Associate Editors
Stephen Duffull, PhD
Stephen Duffull is a Professor of Clinical Pharmacy and Dean of the
School of Pharmacy at the University of Otago, Dunedin, New
Zealand. He runs a modeling and simulation lab within the School of
Pharmacy. Research interests include optimal design, MCMC methods
particularly in clinical toxicology and haemostasis. He has been
involved in the area of PKPD and nonlinear mixed effects modeling
for 20 years. Currently his research involves the development of
pharmacological models, modeling of data and the design of clinical
studies. These foci essentially revolve around the therapeutic
areas of coagulation, malaria and clinical toxicology.
Douglas A. Lauffenburger, PhD
Dr. Lauffenburger is Ford Professor of Bioengineering and Head of
the Department of Biological Engineering at MIT, and also holds
appointments in the Department of Biology and the Department of
Chemical Engineering. He is a member of the Koch Institute for
Integrative Cancer Research, the Center for Biomedical Engineering,
the Center for Environmental Health Sciences, and the Center for
Gynepathology Research, and is Director of the Computational &
Systems Biology Initiative. He earned BS and PhD degrees in
chemical engineering from the University of Illinois and the
University of Minnesota, in 1975 and 1979, respectively. His major
research interests are in cell engineering: the fusion of
engineering with molecular cell biology. Dr. Lauffenburger is a
member of the National Academy of Engineering and of the American
Academy of Arts & Sciences, and has served as President of the
Biomedical Engineering Society, Chair of the College of Fellows of
AIMBE, and on the Advisory Council for the National Institute for
General Medical Sciences at NIH.
Lang Li, PhD
Lang Li, PhD, is an Associate Professor in the Department of
Medical and Molecular Genetics in the Indiana University School of
Medicine (IUSM). He received his PhD in Biostatistics from the
University of Michigan in Ann Arbor, Michigan, before joining the
IUSM in 2001. Dr. Li is the Interim Director of the Center for
Computational Biology and Bioinformatics in the IUSM, and the
Associate Director of the Indiana Institute of Personalized
Medicine (IIPM). He uses informatics, genomics and statistics to
investigate drug efficacy and safety problems. He is interested in
both the molecular mechanisms and clinical significance of drug
safety and efficacy.
Donald Mager, PharmD, PhD
Dr. Mager is an Associate Professor of Pharmaceutical Sciences at
the University at Buffalo, State University of New York (UB). He
received his BS degree in Pharmacy from UB in 1991, followed by the
PharmD (2000) and PhD (2002) degrees. Prior to joining the faculty
at UB, he completed two years of post-doctoral training as an IRTA
Fellow at the National Institute on Aging of the NIH, where he
continued to serve as a special volunteer from 2004 to 2010. He
received the University at Buffalo Young Investigator Award in 2006
and the New Investigator Award in Pharmacokinetics,
Pharmacodynamics, and Drug Metabolism from AAPS in 2007. He
currently serves on the Clinical Pharmacology Advisory Committee to
the FDA and the Editorial Advisory Boards of Biopharmaceutics and
Drug Disposition and Journal of Pharmacokinetics and
Pharmacodynamics. He was also elected as a Fellow to the American
College of Clinical Pharmacology, as Chair of the Clinical
Pharmacology and Translational Research section of AAPS, and as a
member of the Board of Directors to the International Society of
Pharmacometrics. His research focuses on identifying molecular and
physiological factors that control the pharmacological properties
of various drugs including anti-cancer, immunomodulatory, and
anti-platelet drugs.
France Mentr&, MD, PhD
Dr. Mentr& is a Professor of Biostatistics in the School of
Medicine of University Paris Diderot (Paris 7). She heads an INSERM
research team on Biostatistical Modelling and Pharmacometrics. She
has worked on development and application of methods for nonlinear
mixed-effects models in pharmacokinetics and pharmacodynamics for
more than 25 years. She is involved in the development of the
software PFIM for optimal design. Dr. Mentr& has co-authored more
than 150 articles in biostatistics, pharmacometrics, clinical
pharmacology and medicine.
Vikram Sinha, PhD
Dr. Sinha is the AVP, Quantitative Pharmacology and Pharmacometrics
at Merck & Co. In his current role he leads a multidisciplinary
he leads a multidisciplinary team of quantitative clinical
pharmacologists, statisticians, engineers, and data management
experts. The Division plays a critical role in understanding the
impact of variability in response to drugs and relates it to
assessing benefit and risk. Previously, Vikram was the Director,
Division of Pharmacometrics, USFDA where pharmacometric work was
conducted with the intent to aid the decision to approve and label
the drug product. There is particular attention on providing a
consulting function on drug dosing for patients and advice on trial
design decisions by sponsors. Previously, Vikram was at Eli Lilly,
where he was scientific lead for global pharmacokinetics,
pharmacodynamics and pharmacometrics. At Lilly, he was accountable
for developing quantitative translational strategies, clinical
plans, and regulatory strategies in the area of clinical
pharmacology. He has 16 years of experience in the pharmaceutical
industry and over 3 years of experience in a regulatory setting. He
has made notable contributions to the general scientific community
through teaching, publications, and engagement with industry and
government consortia dedicated to advancing innovation in the area
of drug discovery and development. Vikram earned a bachelor&s
degree in pharmacy and a doctorate degree in pharmaceutical
sciences from the University of Arizona. He completed post-doctoral
training at the University of Nebraska Medical Center.
Paolo Vicini, PhD
Dr. Vicini is a Senior Director in the Department of Clinical
Pharmacology and DMPK at MedImmune in Cambridge, UK. He received
his PhD in bioengineering from the Polytechnic of Milan in 1996. In
2003, he received the IEEE Engineering in Medicine and Biology
Early Career Achievement Award. His previous research focus was on
the development of data analysis software and the application of
modeling and simulation to glucose and insulin metabolism, cancer,
pharmacokinetics and pharmacodynamics. Since his move to Pfizer in
2008, his work has focused on translational modeling and simulation
in support of various discovery programs. He has published more
than 100 articles employing diverse modeling and simulation
technology on a variety of applications.
Ping Zhao, PhD
Dr. Zhao is currently the Scientific Lead of PBPK
(physiologically-based pharmacokinetic modeling) Program in the
Division of Pharmacometrics, Office of Clinical Pharmacology at US
Food and Drug Administration. He is responsible for assessing PBPK
analyses in IND and NDA submissions. Ping&s research focuses on
understanding the effect of intrinsic and/or extrinsic patient
factors on drug exposure-response using PBPK models. Prior to 2008,
he worked as a clinical pharmacologist at Amgen in Seattle, WA
(2008), a pharmacokineticist at Sonus Pharmaceuticals in Seattle,
WA (), and a DMPK scientist at Pfizer in La Jolla, CA
(). Ping obtained his BS in Pharmacy from Beijing Medical
University in China in 1994, and his PhD in Pharmaceutics from
University of Washington in Seattle, WA, USA in 2002.
Editorial Board
Sandra Allerheiligen, PhD
Merck Research Laboratories
West Point, PA, USA
Ioannis Androulakis, PhD
Rutgers University Surgery, UMDNJ-RWJ Medical School
Piscataway Township, NJ, USA
Joseph P Balthasar, PhD
University of Buffalo
Buffalo, NY, USA
Jeffrey S. Barrett, PhD, FCP
The Children's Hospital of Philadelphia
Philadelphia, PA, USA
Robert Bies, PharmD, PhD
Indiana University
Bloomington, IN, USA
Kim L. R. Brouwer, PharmD, PhD
University of North Carolina at Chapel Hill
Chapel Hill, NC, USA
Jenny Chien, PhD
Eli Lilly Co.
Clinton, IN, USA
David Z. D'Argenio, PhD
University of Southern California
Los Angeles, CA, USA
Oleg Demin, PhD
CSO Institute for Systems Biology SPb
Moscow, Russia
Paolo Denti, PhD
University of Cape Town
Cape Town, South Africa
Hartmut Derendorf, PhD
University of Florida
Gainesville, FL, USA
James M. Gallo, PharmD, PhD
Albany College of Pharmacy and Health Sciences
Albany, NY, USA
Christine Garnett, PhD
St Louis, MO, USA
David Gavaghan, PhD
University of Oxford
Oxford, United Kingdom
Ekaterina Gibiansky, PhD
QuantPharm LLC
North Potomac, MD, USA
Pascal Girard, PhDMerck Institute for
Pharmacometrics - Merck Sereno S.A.
Lausanne, Switzerland
Bart Hendriks, PhD
Merrimack Pharmaceuticals
Cambridge, MA, USA
Nicholas H.G. Holford, MBChB
The University of Auckland
Auckland, New Zealand
Brett Howell, PhDThe Hamner-UNC Institute for Drug
Safety Sciences
Research Triangle Park, NC, USA
Matt Hutmacher, PhD
Ann Arbor Pharmacometrics Group
Ann Arbor, MI, USA
Jin Yan Jin, PhD
Genentech, Inc
San Francisco, CA, USA
Kristin Karlsson, PhD
Uppsala University
Uppsala, Sweden
Mats Olof Karlsson, PhD
Uppsala University
Uppsala, Sweden
Ron Keizer, PhDInsightRX
San Francisco, CA, USA
Douglas Kell, Dphil
Manchester Institute of Biotechnology
Manchester, UK
Terrence Kenakin, PhD
University of North Carolina, Chapel Hill
Chapel Hill, NC, USA
Steven E. Kern, PhDBill & Melinda Gates
Foundation
Seattle, WA, USA
Hiroaki Kitano, PhD
The Systems Biology Institute
Tokyo, Japan
Charlotte Kloft, PhD
Freie Universitaet Berlin
Berlin, Germany
Joerg Lippert, PhD
Bayer Healthcare Pharmaceuticals
Leverkusen, Germany
Phil Lowe, PhD
Novartis Pharma AG
Basel, Switzerland
Wei Lu, PhD
Peking University/Pfizer Pharmacometrics
Beijing, China
Efthymios Manolis, MSc
European Medicines Agency
London, United Kingdom
Peter Milligan, PhD
Pfizer Global Research and Development
London, United Kindgdom
Diane R Mould, PhD, FCP
Projections Research Inc.
Phoenixville, PA, USA
Jerry Nedelman, PhD
Novartis Pharmaceuticals Corporation
East Hanover, NJ, USA
Kyungsoo Park, MD, PhD
Yonsei University College of Medicine
Seoul, Republic of Korea
Marc Pfister, MD, FCP
University of Basel
Basel, Switzerland
Jose Pinheiro, PhD
Johnson and Johnson Pharmaceutical Research
Raritan, NJ, USA
Amin Rostami-Hodjegan, PharmD, PhD
University of Manchester
Manchester, United Kingdom
Malcolm Rowland, DSc, PhD
University of Manchester
Manchester, United Kingdom
University of California, San Francisco
San Francisco, CA, USA
Radojka Savic, PhD
University of California
Oakland CA, USA
Stephan Schmidt, PhD
University of Florida
Orlando, FL USA
Virginia D. Schmith, PhD, FCP
GlaxoSmithKline
Zebulon, NC, USA
Brian Smith, PhD
Novartis Institutes of Biomedical Research, Inc.
Cambridge, MA, USA
Peter Sorger, PhD
Harvard Medical School
Cambridge, MA, USA
Joe Standing, PhD
University College London
London, United Kingdom
Yuichi Sugiyama, PhD
Riken Innovation Center
Sugiyama Laboratory
Yokohama, Japan
Hiroshi Suzuki, PhDThe University of Tokyo
Tokyo, Japan
Joel Tarning, PhD Mahidol-Oxford Tropical
Medicine Research Unit
Bangkok, Thailand
Nicholas Tatonetti, PhD
Columbia University
New York, NY, USA
I&aki F. Troc&niz, PharmD, PhD
University of Navarra
Pamplona, Spain
An Vermeulen, PhD
Janssen Research and Development
Beerse, Belgium
Alexander A. Vinks, PharmD, PhD, FCP
University of Cincinnati, College of Medicine
Cincinnati, OH, USA
Hua Xu, PhD
University of Texas Health Science Center
Houston, Texas, USA
Ping Zhang, PhD
IBM T. J. Watson Research Center
Yorktown Heights, NY, USA
A journal of the American Society for Clinical Pharmacology and Therapeutics (ASCPT)}