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• E.g. onWindowswithJava1.6orlater,ifyouhavecheckedoutthesourceatC:\code\loci,setyourCLASS-
PATHenvironmentvariabletothevalueC:\code\loci\jar\*;C:\code\loci.Youcanaccesstheenviron-
mentvariableconfigurationareabyright-clickingonMyComputer,choosingProperties,Advancedtab,Environment
Variablesbutton.
2. Compilethesourcewithant compile.
3. SettheLOCI_DEVELenvironmentvariabletoanyvalue(thevariablejustneedstobedefined).
8.2 FARSIGHT
FARSIGHT
4
isacollectionofmodulesforimageanalysiscreatedbyLOCI’scollaboratorsattheUniversityofHouston
5
.These
opensourcemodulesarebuiltontheITK libraryandthuscantakeadvantageofITK’ssupportforBio-Formatstoprocess
otherwiseunsupportedimageformats.
TheprincipalFARSIGHTmodulethatbenefitsfromBio-FormatsistheNucleusEditor
6
,thoughinprincipleanyFARSIGHT-
basedcodethatreadsimageformatsviathestandardITKmechanismwillbeabletoleverageBio-Formats.
SeeAlso:
FARSIGHTDownloadspage
7
FARSIGHTHowToBuildtutorial
8
8.3 i3dcore
i3dcore
9
,alsoknownastheCBIA3Dimagerepresentationlibrary,isa3DimageprocessinglibrarydevelopedattheCentre
forBiomedicalImageAnalysis
10
. Togetherwithi3dalgo
11
andi4dcore
12
,i3dcoreformsacontinuouslydevelopedtemplated
cross-platformC++suiteoflibrariesformultidimensionalimageprocessingandanalysis.
i3dcoreiscapableofreadingimageswithBio-FormatsusingJavaforC++
13
(java4cpp).
SeeAlso:
Downloadi3dcore
14
CBIASoftwareDevelopment
15
8.4 ImgLib
ImgLib216isamultidimensionalimageprocessinglibrary.Itprovidesageneralmechanismforwritingimageanalysisalgorithms,
withoutwritingcaselogicforbitdepth
17
,orworryingaboutthesourceofthepixeldata(arraysinmemory,filesondisk,etc.).
TheSCIFIO
18
projectprovidesanImgOpener
19
utilityclassforreadingdataintoImgLib2datastructuresusingBio-Formats.
4
http://www.farsight-toolkit.org/
5
http://www.uh.edu/
6
http://www.farsight-toolkit.org/wiki/NucleusEditor
7
http://www.farsight-toolkit.org/wiki/Special:FarsightDownloads
8
http://www.farsight-toolkit.org/wiki/FARSIGHT_HowToBuild
9
http://cbia.fi.muni.cz/user_dirs/i3dlib_doc/i3dcore/index.html
10
http://cbia.fi.muni.cz/software-development.html
11
http://cbia.fi.muni.cz/user_dirs/i3dlib_doc/i3dalgo/index.html
12
http://cbia.fi.muni.cz/user_dirs/of_doc/libi4d.html
13
http://java4cpp.kapott.org/
14http://cbia.fi.muni.cz/user_dirs/i3dlib_doc/i3dcore/index.html#download
15
http://cbia.fi.muni.cz/software-development.html
16
http://imglib2.net/
17http://en.wikipedia.org/wiki/Color_depth
18http://scif.io/
19https://github.com/scifio/scifio/blob/master/scifio/src/main/java/io/scif/img/ImgOpener.java
8.2. FARSIGHT
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8.5 ITK
TheInsightToolkit
20
(ITK)isanopen-source,cross-platformsystemthatprovidesdeveloperswithanextensivesuiteofsoftware
toolsforimageanalysis. Developedthroughextremeprogrammingmethodologies,ITKemploysleading-edgealgorithmsfor
registeringandsegmentingmultidimensionaldata.
ITK providesanImageIO plug-instructurethatworksviadiscoverythroughadependencyinjectionscheme. Thisallowsa
programbuiltonITKtoloadplug-insforreadingandwritingdifferentimagetypeswithoutactuallylinkingtotheImageIO
librariesrequiredforthosetypes. Suchencapsulationautomaticallygrantstwomajorboons: firstly, programscanbeeasily
extendedjustbyvirtueofusingITK(developersdonothavetospecificallyaccommodateoranticipatewhatplug-insmaybe
used).Secondly,thearchitectureprovidesadistributionmethodforopensourcesoftware,likeBio-Formats,whichhavelicenses
thatmightotherwiseexcludethemfrombeingusedwithothersoftwaresuites.
TheSCIFIOImageIO
21
pluginprovidesanforITKimageIObasethatusesBio-Formats
22
toreadandwritesupportedlifesciences
fileformats.ThispluginallowsanyprogrambuiltonITKtoreadanyoftheimagetypessupportedbyBio-Formats.
8.5.1 Prerequisites
YoushouldhaveCMake
23
installed,toallowtheconfigurationofITKbuilds.IfyouwantthelatestITKdevelopmentbuild,you
willneedGit
24
aswell.
8.5.2 Installation
SimplydownloadITKfromtheKitwaresoftwarepage
25
.UsingCMake,setthefollowingconfigurationflag:
(NOTE:thisflagisonlyvisiblein“advanced”modewithinCMake)
• Fetch_SCIFIO=ON
IfyouwouldliketousetheutilityclassesincludedwiththeSCIFIOimageIO,alsosettheflag:
• BUILD_TESTING=ON
ThenbuildITKasnormal.ItwillautomaticallydownloadandbuildthelatestSCIFIOimageIOplugin.Usage
ApplicationsusingtheinstalledITKshouldautomaticallydefertotheSCIFIOImageIO,andthusBio-Formats,whenreadingor
savingimagesnotnativelysupportedbyITK.
TousetheSCIFIOtestutility,run:
ITKIOSCIFIOTestDriver
fromyour${ITK_BUILD}/bindirectory.Thisprogramhasfourseparateapplicationsthatcanbedirectlyinvokedusingthesyntax:
ITKIOSCIFIOTestDriver [Program to run] [Program arguments]
Theprogramsareasfollows:
• itkSCIFIOImageInfoTest-DisplaysbasicinformationtoverifytheSCIFIOimageIOworks,using.fakeimages.
• itkSCIFIOImageIOTest-Readsaninputimage,andwritesitoutasaspecifiedtype
• itkRGBSCIFIOImageTest-SameasitkSCIFIOImageIOTestbutforRGB26 types
• itkVectorImageSCIFIOImageIOTest-SameasitkSCIFIOImageIOTestbutforVectorImage
27
type
20
http://itk.org/
21
https://github.com/scifio/scifio-imageio
22
http://farsight-toolkit.org/wiki/Bio-Formats
23
http://www.cmake.org/
24
http://git-scm.com/
25
http://www.itk.org/ITK/resources/software.html
26
http://www.itk.org/Doxygen/html/classitk_1_1RGBPixel.html
27
http://www.itk.org/Doxygen/html/classitk_1_1VectorImage.html
8.5. ITK
45
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Forexample,toconverta.cziimagetoa.tif,youwoulduse:
ITKIOSCIFIOTestDriver itkSCIFIOImageIOTest in.czi out.tif
8.5.3 Troubleshooting
Pleasesendanyissues,suggestionsorrequeststotheinsightusersmailinglist
28
.
8.6 QuforMATLAB
QuforMATLAB29 isaMATLABtoolboxforthevisualizationandanalysisofN-dimensionaldatasetstargetedtothefieldof
biomedicalimaging,developedbyAaronPonti.
• UsesBio-Formatstoreadfiles
• OpensourcesoftwareavailableundertheMozillaPublicLicense
SeeAlso:
QuforMATLABdownloadpage
30
8.7 Subimager
Subimager
31
,theSUBprocessIMAGEservER,isanHTTPserverthatusesBio-Formatsasaback-endtoserve.TIFimages.
SubimagerisdesignedtoberunasasubprocessofCellProfilertoprovideCellProfilerwiththecapabilitytoreadandwritea
varietyofimageformats. Itcanbeusedasastand-aloneimageserver. ItwasdevelopedbytheBroadInstitute
32
tofacilitate
integrationwiththeirCellProfiler33 imageanalysisapplication.
28
http://www.itk.org/ITK/help/mailing.html
29
http://www.scs2.net/home/index.php?option=com_content&view=article&id=46%3Aqu-for-matlab&catid=34%3Aqu&Itemid=55
30
http://www.scs2.net/home/index.php?option=com_content&view=article&id=46%3Aqu-for-matlab&catid=34%3Aqu&Itemid=55&limitstart=3
31
https://github.com/CellProfiler/subimager
32
http://www.broadinstitute.org/
33
http://www.cellprofiler.org/
8.6. QuforMATLAB
46
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CHAPTER
NINE
NUMERICAL DATA PROCESSING
APPLICATIONS
9.1 IDL
IDL
1
(InteractiveDataLanguage)isapopulardatavisualizationandanalysisplatformusedforinteractiveprocessingoflarge
amountsofdataincludingimages.
IDLpossessestheabilitytointeractwithJavaapplicationsviaitsIDL-Javabridge.KarstenRodenackerhaswrittenascriptthat
usesBio-FormatstoreadinimagefilestoIDL.
9.1.1 Installation
Downloadtheij_read_bio_formats.pro
2
scriptfromKarstenRodenacker’sIDLgoodies(?)
3
website. Seethecommentsatthe
topofthescriptforinstallationinstructionsandcaveats.
9.1.2 Upgrading
TouseanewerversionofBio-Formats,overwritetherequisiteJARfileswiththenewerversion
4
andrestartIDL.
9.2 KNIME
KNIME
5
(KonstanzInformationMiner)isauser-friendlyandcomprehensiveopen-sourcedataintegration,processing,analysis,
andexplorationplatform.KNIMEsupportsimageimportusingBio-FormatsusingtheKNIMEImageProcessing
6
(a.k.a.KNIP)
plugin.
9.3 MATLAB
MATLABisahigh-levellanguageandinteractiveenvironmentthatfacilitatesrapiddevelopmentofalgorithmsforperforming
computationallyintensivetasks.
CallingBio-FormatsfromMATLABisfairlystraightforward,sinceMATLABhasbuilt-ininteroperabilitywithJava. Wehave
createdasetofscripts
8
forreadingimagefiles.NotetheminimumsupportedMATLABversionisR2007b(7.5).
1
http://www.exelisvis.com/ProductsServices/IDL.aspx
2
http://www.helmholtz-muenchen.de/ibb/homepage/karsten.rodenacker/IDL/_pro/ij_read_bio_formats.pro
3
http://www.helmholtz-muenchen.de/ibb/homepage/karsten.rodenacker/IDL/index.php
4
http://downloads.openmicroscopy.org/bio-formats/
5
http://knime.org/
6
http://tech.knime.org/community/image-processing
7
http://www.mathworks.com/products/matlab/
8
https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats/matlab
47
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9.3.1 Installation
DownloadtheMfiles
9
andloci_tools.jar
10
andplacetheminyourMATLABworkdirectory.
9.3.2 Usage
PleaseseetheBio-FormatsMATLABGuideforusageinstructions. Ifyouintendtoextendtheexisting.mfiles,pleasealsosee
thedeveloperpageformoreinformationonhowtouseBio-Formatsingeneral.
9.3.3 Performance
Inourtests(MATLABR14vs.java1.6.0_20),thescriptexecutesatapproximatelyhalfthespeedofourshowinfcommandline
tool,duetooverheadfromcopyingarrays.
9.3.4 Upgrading
TouseanewerversionofBio-Formats,overwriteloci_tools.jarwiththenewerversion
11
andrestartMATLAB.
9.3.5 Alternativescripts
SeveralothergroupshavedevelopedtheirownMATLABscriptsthatuseBio-Formats,includingthefollowing:
• https://github.com/prakatmac/bf-tools/
• http://www.mathworks.com/matlabcentral/fileexchange/32920-imread-for-multiple-life-science-image-file-formats
9.4 VisAD
TheVisAD
12
visualizationtoolkitisaJavacomponentlibraryfor interactiveandcollaborativevisualizationandanalysisof
numericaldata.VisADusesBio-Formatstoreadmanyimageformats,notablyTIFF.
9.4.1 Installation
Thevisad.jarfilehasBio-Formatsbundledinside,sonofurtherinstallationisnecessary.
9.4.2 Upgrading
Itshouldbepossibletouseanewerversionof Bio-Formatsbyputtingthelatestloci_tools.jar
13
orbio-formats.jar
14
before
visad.jarintheclasspath.Alternately,youcancreatea“VisADLite”usingthemake litecommandfromVisADsource,and
usetheresultantvisad-lite.jar,whichisastrippeddownversionofVisADwithoutsampleapplicationsorBio-Formatsbundled
in.
9
https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats/matlab
10
http://downloads.openmicroscopy.org/bio-formats/
11
http://downloads.openmicroscopy.org/bio-formats/
12
http://www.ssec.wisc.edu/%7Ebillh/visad.html
13
http://downloads.openmicroscopy.org/bio-formats/
14
http://downloads.openmicroscopy.org/bio-formats/
9.4. VisAD
48
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CHAPTER
TEN
VISUALIZATION AND ANALYSIS
APPLICATIONS
10.1 BitplaneImaris
Imaris
1
isBitplane’scorescientificsoftwaremodulethatdeliversallthenecessaryfunctionalityfordatavisualization,analysis,
segmentationandinterpretationof3Dand4Dmicroscopydatasets.Combiningspeed,precisionandease-of-use,Imarisprovides
acompletesetoffeaturesforworkingwiththree-andfour-dimensionalmulti-channelimagesofanysize,fromafewmegabytes
tomultiplegigabytesinsize.
Asofversion7.2
2
,ImarisintegrateswithFiji,whichincludesBio-Formats.Seethispage
3
foradetailedlistofImaris’features.
10.2 CellProfiler
CellProfiler
4
—developedbytheBroadInstitute
5
‘sImagingPlatform
6
—isfreeopen-sourcesoftwaredesignedtoenablebiologists
withouttrainingincomputervisionorprogrammingtoquantitativelymeasurephenotypesfromthousandsofimagesautomati-
cally.CellProfilerusesBio-Formatstoreadimagesfromdisk,aswellaswritemovies.
10.2.1 Installation
TheCellProfilerdistributioncomeswithBio-Formatsincluded,sonofurtherinstallationisnecessary.
10.2.2 Upgrading
ItshouldbepossibletouseanewerversionofBio-Formatsbyreplacingthebundledloci_tools.jarwithanewerversion.
• Forexample,onMacOSX,Ctrl+clicktheCellProfilericon,chooseShowPackageContents,andreplacethefollowing
files:
– Contents/Resources/bioformats/loci_tools.jar
– Contents/Resources/lib/python2.5/bioformats/loci_tools.jar
SeeAlso:
CellProfilerwebsite
7
1http://www.bitplane.com/
2http://www.bitplane.com/go/releasenotes?product=Imaris&version=7.2&patch=0
3http://www.bitplane.com/imaris/imaris
4
http://www.cellprofiler.org/
5http://www.broadinstitute.org/
6
http://www.broadinstitute.org/science/platforms/imaging/imaging-platform
7
http://www.cellprofiler.org/
49
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10.3 Comstat2
Comstat2isaJava-basedcomputerprogramfortheanalysisandtreatmentofbiofilmimagesin3D.ItistheMaster’sprojectof
MartinVorregaard
8
.
Comstat2usestheBio-FormatsImporterpluginforImageJtoreadfilesinTIFFandLeicaLIFformats.
SeeAlso:
Comstat2-amodern3Dimageanalysisenvironmentforbiofilms9
10.4 Endrov
Endrov
10
(orhttp://www.endrov.net)(EV)isamulti-purposeimageanalysisprogramdevelopedbytheThomasBurglingroup
11
atKarolinskaInstitute
12
,DepartmentofBiosciencesandNutrition.
10.4.1 Installation
TheEVdistributioncomesbundledwiththecoreBio-Formatslibrary(bio-formats.jar),sonofurtherinstallationisnecessary.
10.4.2 Upgrading
ItshouldbepossibletouseanewerversionofBio-Formatsbydownloadingthelatest4.4. versionofthebio-formats.jar13 and
puttingitintothelibsfolderoftheEVdistribution,overwritingtheoldfile.
Youcouldalsoincludesomeoptionallibraries,toaddsupportforadditionalformats,ifdesired.
10.5 FocalPoint
FocalPoint
14
isanimagebrowser,similartoWindowsExplorer
15
orotherfilemanager
16
application,specificallydesignedto
workwithmorecompleximagetypes.FocalPointusesBio-Formatstogeneratethumbnailsforsomeformats.
10.5.1 Installation
FocalPointisbundledwithBio-Formats,sonofurtherinstallationisnecessary.
10.5.2 Upgrading
ItshouldbepossibletouseanewerversionofBio-Formats
17
byoverwritingtheoldloci_tools.jarwithintheFocalPointdistribu-
tion.ForMacOSX,youwillhavetocontrolclicktheFocalPointprogramicon,choose“ShowPackageContents”andnavigate
intoContents/Resources/Javatofindtheloci_tools.jarfile.
8
http://www.comstat.dk/
9
http://www2.imm.dtu.dk/pubdb/views/publication_details.php?id=5628
10
https://github.com/mahogny/Endrov
11
http://www.biosci.ki.se/groups/tbu
12
http://www.ki.se/
13
http://downloads.openmicroscopy.org/bio-formats/
14
http://www.bioinformatics.bbsrc.ac.uk/projects/focalpoint/
15
http://en.wikipedia.org/wiki/Windows_Explorer
16
http://en.wikipedia.org/wiki/File_manager
17http://downloads.openmicroscopy.org/bio-formats/
10.3. Comstat2
50
10.6 GraphicConverter
GraphicConverter
18
isaMacOSapplicationforopening,editing,andorganizingphotos.Versions6.4.1andlateruseBio-Formats
toopenallfileformatssupportedbyBio-Formats.
10.7 Icy
Icy
19
isanopen-sourceimageanalysisandvisualizationsoftwarepackagethatcombinesauser-friendlygraphicalinterfacewith
theabilitytowritescriptsandpluginsthatcanbeuploadedtoacentralizedwebsite. ItusesBio-Formatsinternallytoreadimages
andacquisitionmetadata,sonofurtherinstallationisnecessary.
10.8 imago
Mayachitraimago20 isanadvanceddesktopimagemanagementpackagethatenablesscientiststoeasilystore,manage,search,
andanalyze5Dbiologicalimagesandtheiranalysisresults.imagointegratesflexibleannotationandmetadatamanagementwith
advancedimageanalysistools.
imagousesBio-Formatstoreadfilesinsomeformats,includingBio-RadPIC,Image-ProWorkspace,MetamorphTIFF,Leica
LCSLEI,OlympusFluoViewFV1000,NikonNIS-ElementsND2,andZeissLSM.
Afree30-daytrialversionofimagoisavailablehere
21
.
10.9 Iqm
Iqm
22
isanimageprocessingapplicationwritteninJava.ItismainlyconstructedaroundtheJavaJAIlibraryandfurthermoreit
incorporatesthefunctionalityofthepopularImageJimageprocessingsoftware.
BecauseiqmintegrateswithImageJ,itcantakeadvantageoftheBio-FormatsImageJplugintoreadimagedata.
10.10 Macnification
Macnification
23
isaMacOSXapplicationfororganizing,editing,analyzingandannotatingmicroscopicimages,designedfor
easeofuse.ItisbeingdevelopedbyOrbicule
24
.
MacnificationusesBio-Formatstoreadfilesinsomeformats,includingGatanDM3,ICS,ImageProSEQ,ImageProIPW,Meta-
morphSTK,OME-TIFFandZeissLSM.
SeeAlso:
Freetrialdownload
25
10.11 MIPAV
TheMIPAV
26
(MedicalImageProcessing,Analysis,andVisualization)application—developedattheCenterforInformation
Technology
27
attheNationalInstitutesofHealth
28
—enablesquantitativeanalysisandvisualizationofmedicalimagesofnumerous
18http://www.lemkesoft.com
19
http://icy.bioimageanalysis.org/
20
http://mayachitra.com/imago/index.html
21
http://mayachitra.com/imago/download-trial.php
22
http://code.google.com/p/iqm/
23
http://www.orbicule.com/macnification/
24
http://www.orbicule.com
25
http://www.orbicule.com/macnification/download
26
http://mipav.cit.nih.gov/
27
http://cit.nih.gov/
28
http://nih.gov/
10.6. GraphicConverter
51
modalitiessuchasPET,MRI,CT,ormicroscopy.YoucanuseBio-FormatsasapluginforMIPAVtoreadimagesintheformats
itsupports.
10.11.1 Installation
FollowthesestepstoinstalltheBio-FormatspluginforMIPAV:
1. Downloadloci_tools.jar
29
anddropitintoyourMIPAVfolder.
2. Downloadthepluginsourcecode
30
intoyourusermipav/pluginsfolder.
3. Fromthecommandline,compilethepluginwith:
cd mipav/plugins
javac -cp $MIPAV:$MIPAV/loci\_tools.jar \\
PlugInBioFormatsImporter.java
4. where$MIPAVisthelocationofyourMIPAVinstallation.
5. Addloci_tools.jartoMIPAV’sclasspath:
• Howtodosodependsonyourplatform.
• E.g.,inMacOSX,editthemipav.app/Contents/Info.plistfile.
6. RunMIPAVandanew“BioFormatsImporter-readimage”menuitemwillappearinthePlugins>Filesubmenu.
Seethereadmefile
31
formoreinformation.
Toupgrade,justoverwritetheoldloci_tools.jarwiththelatestone
32
. YoumaywanttodownloadthelatestversionofMIPAV
first,totakeadvantageofnewfeaturesandbug-fixes.
10.12 Vaa3D
Vaa3D33,developedbythe PengLab34 attheHHMIJaneliaFarmResearchCampus35,isahandy,fast,andversatile3D/4D/5D
ImageVisualization&AnalysisSystemforBioimages&SurfaceObjects.
Vaa3DcanuseBio-FormatsviatheBio-FormatsC++bindings
36
toreadimages.
10.13 VisBio
VisBio
37
isabiologicalvisualizationtooldesignedforeasyvisualizationandanalysisofmultidimensionalimagedata. VisBio
usesBio-FormatstoimportfilesastheBio-Formatslibraryoriginallygrewoutofoureffortstocontinuallyexpandthefileformat
supportwithinVisBio.
10.13.1 Installation
VisBioisbundledwithBio-Formats,sonofurtherinstallationisnecessary.
29http://downloads.openmicroscopy.org/bio-formats/
30https://github.com/openmicroscopy/bioformats/blob/develop/components/scifio/utils/mipav/PlugInBioFormatsImporter.java
31
https://github.com/openmicroscopy/bioformats/blob/develop/components/scifio/utils/mipav/readme.txt
32
http://downloads.openmicroscopy.org/bio-formats/
33
http://vaa3d.org
34
http://penglab.janelia.org/
35
http://www.hhmi.org/janelia/
36
http://www.farsight-toolkit.org/wiki/FARSIGHT_Tutorials/Building_Software/Bio-Formats/Building_C%2B%2B_Bindings
37
http://www.loci.wisc.edu/visbio/
10.12. Vaa3D
52
10.13.2 Upgrading
ItshouldbepossibletouseanewerversionofBio-Formats
38
byoverwritingtheoldbio-formats.jarandoptionallibrarieswithin
theVisBiodistribution.ForMacOSX,you’llhavetocontrolclicktheVisBioprogramicon,choose“ShowPackageContents”
andnavigateintoContents/Resources/JavatofindtheJARfiles.
10.14 XuvTools
XuvTools
39
isautomated3Dstitchingsoftwareforbiomedicalimagedata. Asofrelease1.8.0,XuvToolsusesBio-Formatsto
readimagedata.
38
http://downloads.openmicroscopy.org/bio-formats/
39
http://www.xuvtools.org
10.14. XuvTools
53
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