ListofFreeSoftwareforMicroscopy

CompiledbyRainerHeintzmann(KingsCollege)fortheAQLMcourse,2009

Micromanager http://www.micromanager.org/ CamAcqJ(GrantHarris) Acquisition&Instrumentcontrol.SupportsQImagingandLuminaracamerasand variableretardersandstages. http://www.mbl.edu/research/labs/adlc/CamAcqJ/ ScanImage(VijayIyer,KarelSwoboda) Developedfor2photonmicroscopyandneurobiology/patchclamping http://research.janelia.org/wiki/display/ephus/ScanImage DisplayandSegmentaton BioimageXD 3DVisualisationandanalysis(nicerendering) UniversityofTurku&UniversityofJyvskyl,Finland Linux/Mac/Windows,VTK+Pythonbased(latestupdate:20080328) http://www.bioimagexd.net VisBio(CurtisRueden&AbrahamSorber), 3DVisualisationandanalysis(nicerendering). InterfaceswithOME.(latestupdate:9Mar2009), http://www.loci.wisc.edu/visbio/ V3D(HanchuanPeng) Greattoolsforvisualizationandsegmentationoflarge(!)datasets. 3Dannotation,landmarking,datamanagement,cellsegmentation,neurontracing, deformableregistration,andmore(latestupdate2009May5) http://hanchuan.peng.googlepages.com ImageProcessing COSMOS=COSMOpenSouce(ChrysanthePreza) soontocome.Havealookat:,http://cirl.memphis.edu/cosmos ImageJ:ApublicdomainJavaimageprocessingprograminspiredbyNIHImage fortheMacintosh.Windows,MacOS,MacOSXandLinux. Plugins(http://rsb.info.nih.gov/ij/plugins/)supportvariousmicroscopyrelated issues.E.g.timestamping,resampling,tracking,LOOKHEREFIRST http://rsb.info.nih.gov/ij/ Dataacquisition

 DeconvolutionLab(GuillaumeSchmit,EPFL) ToolboxforImageJwithvariousdeconvolutionalgorithms.Someofthemarestate oftheartwaveletbasedconstraints.Only2^nsizedimages! AskDanielSage(daniel.sage@epfl.ch),EPFLifinterestedinusing. 3D_Deconvolution(PierreBesson,CdricVoneschandFranoisAguet,EPFL) 3DdeconvolutionpackagewithPSFgeneration.Only2^nsizedimages. http://bigwww.epfl.ch/demo/deconvolution3D/ IterativeDeconvolve3D(BobDougherty,OptiNav,Inc.) Memoryintensitve. http://www.optinav.com/imagej.html DeconvolutionJ(NickLinnenbrgger) http://rsb.info.nih.gov/ij/plugins/fftj.html Voxx:AVolumeRenderingProgramfor3DMicroscopy.Voxxisavoxelbased(not surfacebased)3Drenderingprogramwhichhasbeenoptimizedforbiological microscopy.Thissoftwarepermitsresearcherstoperformrealtimerenderingof largemicroscopydatasetsusinginexpensivepersonalcomputers.Wedevelopedit toexplore3Ddatasetscollectedonconfocalandmultiphotonmicroscopysystems, butitcanalsorenderotherkindsofdata(e.g.CT,MRI,etc.). http://www.nephrology.iupui.edu/imaging/voxx/ NIHimage(Maconly):NIHImageisapublicdomainimageprocessingand analysisprogramfortheMacintosh. http://rsb.info.nih.gov/nihimage/ CellProfiler(AnnCarpenter,MIT) Versatile2Dprocessingplatformforhighthroughputscreeningapplications. http://www.cellprofiler.org/ IrfanView+IrfanViewplugins:Batchconversion(withimageprocessing), multipageTIFediting,TIFF,AVI,MPEG,DICOM,(lookunderviewMultipage images,Extractimagesfromamovie, http://www.irfanview.com/ VisBio:VisBioisabiological(3D)visualizationtooldesignedforeasy visualizationandanalysisofmultidimensionalimagedata. http://www.loci.wisc.edu/visbio/ IVE&Priism(Sedatlab,UCSF) http://www.msg.ucsf.edu/IVE/index.html

Tracking CellTracker(HailinShen,Univ.ofManchester) Advancedandusefultoolfor2Dtrackingofcellsandfeatures.UsesSnakes.Based onMatlab.(lastupdate8June,2006) http://dbkgroup.org/celltracker/ utrack(Jaquaman,Danuser) ForexpertspowerfullinkingalgorithminMatlab, 3Dispossible.ManyMatlabtoolboxesareneeded. http://lccb.scripps.edu/content/download.html TrackingandBallonSegmentation,2D(L.Dupuy) Theyalsocandotrackingbutdonotshowitonthewebsite.Worthasking. Segmentationplugingcanbedownloaded: http://www.archiroot.org.uk 3DTracking Websitewasdown.Butshouldbegood.Windowsonly.Zebrafishembryogenesis? http://www.cbiplatform.net/ View5D:JavaApplet,ImageJplugin,Matlabplugin TheprogramView5Dinteractivelydisplaysofupto5dimensionalvolumetric datasets. Threeorthogonalslicingviews,2Dand3Dhistogramsofintensity(scattergrams), Basicimageprocessingoperations(ratioing,..),Interactivecountingandtaggingof entities,Trackingof3Dmovements,Multiplicativedisplayoflifetimeorratio images. http://www.nanoimaging.de/View5D/ VTK:Forprogrammersonly.TheVisualizationToolKit(VTK)isanopensource, freelyavailablesoftwaresystemfor3Dcomputergraphics,imageprocessing, andvisualization.Moreforexpertusers,whoknowhowtoprogram.Very powerfulandbigcommunity! http://www.vtk.org/ BIRN:Selectionofvarioususefultoolsforimageprocessingandanalysis.Mouse BrainAtlas,3DSlicer,LONIPipeline,FunctionalMRI, http://www.nbirn.net/Resources/Downloads/ OME:OpenMicroscopyEnvironment Datamanagementforbiologicallightmicroscopy.Imagebasedanalysisofcellular dynamics.Imagebasedscreensofcellularlocalizationorphenotypes. OMEisadatabaseenginewhichallowsalabtostoreallmicroscopyimagesalong withmetadata;keepingtrackofprojects.Someimageprocessingfeaturesavailable. http://www.openmicroscopy.org/

DIPimage/DIPlib:(Matlabisneededasaplatform) ThisMatlabtoolboxcontainsalargeamountofveryuseful(oftenNdimensional) imageprocessingalgorithms.DIPimagefeaturesitsowndatatype(dip_image)and aconvenientbrowsertoquicklyinvestigatetheresults. MicroscopyorientedFeaturesare:AutomaticThresholdingalgorithms,Cross correlationbasedshiftdetermination,Segmentationalgorithms(e.g.watershed transform),Noisefiltering(e.g.anisotropicdiffusionwithlocalstructuretensors), Convolution,Measurementsoflabeledentities(e.g.Majoraxisdirection) http://www.ph.tn.tudelft.nl/DIPlib/ CudaMat(RainerHeintzmann) UsingNVidiasGPUsforfastdatacrunchinginMatlab. Idea:Makeitsimple:myImage=cuda(myImage); Onlyasubsetsupportedatthemoment.Datatypes:singleandscomplex Contactme(heintzmann@gmail.com) minFunc(MarkSchmidt) Matlabfunctionforgeneralminimization.Lotsofmethodsimplemented. http://www.cs.ubc.ca/~schmidtm/Software/minFunc.html