Bio-Formats Documentation Release 4.4.12 The Open Microscopy Environment September 23, 2014 CONTENTS I About Bio-Formats 2 1 Why Java? 4 2 Bio-Formats metadata processing 5 3 Help 6 3.1 Reporting a bug ................................................... 6 3.2 Troubleshooting ................................................... 7 4 Bio-Formats versions 9 4.1 Version history .................................................... 9 II User Information 24 5 Using Bio-Formats with ImageJ and Fiji 25 5.1 ImageJ ........................................................ 25 5.2 Fiji .......................................................... 26 5.3 Bio-Formats features in ImageJ and Fiji ....................................... 26 5.4 Installing Bio-Formats in ImageJ .......................................... 27 5.5 Using Bio-Formats to load images into ImageJ ................................... 29 5.6 Managing memory in ImageJ/Fiji using Bio-Formats ................................ 32 5.7 Upgrading the Bio-Formats importer for ImageJ to the latest trunk build ...................... 35 6 OMERO 40 7 Image server applications 41 7.1 BISQUE ....................................................... 41 7.2 OME Server ..................................................... 41 8 Libraries and scripting applications 44 8.1 Command line tools ................................................. 44 8.2 FARSIGHT ...................................................... 45 8.3 i3dcore ........................................................ 45 8.4 ImgLib ........................................................ 46 8.5 ITK .......................................................... 46 8.6 Qu for MATLAB ................................................... 47 8.7 Subimager ...................................................... 47 9 Numerical data processing applications 48 9.1 IDL .......................................................... 48 9.2 KNIME ........................................................ 48 9.3 MATLAB ...................................................... 48 9.4 VisAD ........................................................ 49 10 Visualization and analysis applications 50 10.1 Bitplane Imaris .................................................... 50 10.2 CellProfiler ...................................................... 50 10.3 Comstat2 ....................................................... 50 i 10.4 Endrov ........................................................ 51 10.5 FocalPoint ...................................................... 51 10.6 Graphic Converter .................................................. 51 10.7 Icy .......................................................... 52 10.8 imago ......................................................... 52 10.9 Iqm .......................................................... 52 10.10 Macnification ..................................................... 52 10.11 MIPAV ........................................................ 52 10.12 Vaa3D ........................................................ 53 10.13 VisBio ........................................................ 53 10.14 XuvTools ....................................................... 54 III Developer Documentation 55 11 Using Bio-Formats 56 11.1 An in-depth guide to using Bio-Formats ....................................... 56 11.2 Generating test images ................................................ 58 12 Bio-Formats as a Java library 60 12.1 API documentation .................................................. 60 12.2 Examples ....................................................... 61 13 Interfacing from non-Java code 71 13.1 Interfacing with Bio-Formats from non-Java code .................................. 71 13.2 Bio-Formats C++ bindings .............................................. 71 13.3 Build instructions for C++ bindings ......................................... 71 13.4 Building C++ bindings in Windows ......................................... 73 13.5 Building C++ bindings in Mac OS X ........................................ 74 13.6 Building C++ bindings in Linux ........................................... 75 14 SCIFIO 76 14.1 SCientific Imaging Formats Input and Output .................................... 76 15 Writing new Bio-Formats file format readers 77 15.1 Bio-Formats file format reader guide ........................................ 77 16 Contributing to Bio-Formats 81 16.1 Developing Bio-Formats ............................................... 81 16.2 Testing individual commits (internal developers) .................................. 82 16.3 Public test data .................................................... 83 16.4 Bio-Formats service and dependency infrastructure ................................. 86 IV Formats 89 17 Dataset Structure Table 91 17.1 Flex Support ..................................................... 94 18 Supported Formats 95 18.1 3i SlideBook ..................................................... 100 18.2 Andor Bio-Imaging Division (ABD) TIFF ..................................... 101 18.3 AIM ......................................................... 101 18.4 Alicona 3D ...................................................... 102 18.5 Amersham Biosciences Gel ............................................. 103 18.6 Amira Mesh ..................................................... 103 18.7 Analyze 7.5 ...................................................... 104 18.8 Animated PNG .................................................... 105 18.9 Aperio SVS TIFF ................................................... 105 18.10 Applied Precision CellWorX ............................................. 106 18.11 AVI (Audio Video Interleave) ............................................ 107 18.12 Axon Raw Format .................................................. 108 ii 18.13 BD Pathway ..................................................... 108 18.14 Becker & Hickl SPCImage .............................................. 109 18.15 Bio-Rad Gel ..................................................... 110 18.16 Bio-Rad PIC ..................................................... 110 18.17 Bitplane Imaris .................................................... 111 18.18 Bruker MRI ..................................................... 112 18.19 Burleigh ....................................................... 113 18.20 Canon DNG ..................................................... 114 18.21 Cellomics ....................................................... 114 18.22 cellSens VSI ..................................................... 115 18.23 DeltaVision ...................................................... 116 18.24 DICOM ........................................................ 117 18.25 ECAT7 ........................................................ 118 18.26 EPS (Encapsulated PostScript) ............................................ 118 18.27 Evotec/PerkinElmer Opera Flex ........................................... 119 18.28 FEI .......................................................... 120 18.29 FEI TIFF ....................................................... 120 18.30 FITS (Flexible Image Transport System) ...................................... 121 18.31 Gatan Digital Micrograph .............................................. 122 18.32 Gatan Digital Micrograph 2 ............................................. 122 18.33 GIF (Graphics Interchange Format) ......................................... 123 18.34 Hamamatsu Aquacosmos NAF ............................................ 124 18.35 Hamamatsu HIS ................................................... 125 18.36 Hamamatsu ndpi ................................................... 125 18.37 Hamamatsu VMS .................................................. 126 18.38 Hitachi S-4800 .................................................... 127 18.39 ICS (Image Cytometry Standard) .......................................... 127 18.40 Imacon ........................................................ 128 18.41 ImagePro Sequence ................................................. 129 18.42 ImagePro Workspace ................................................. 130 18.43 IMAGIC ....................................................... 130 18.44 IMOD ........................................................ 131 18.45 Improvision Openlab LIFF .............................................. 132 18.46 Improvision Openlab Raw .............................................. 133 18.47 Improvision TIFF .................................................. 133 18.48 InCell 1000 ...................................................... 134 18.49 InCell 3000 ...................................................... 135 18.50 INR .......................................................... 136 18.51 IPLab ......................................................... 136 18.52 IPLab-Mac ...................................................... 137 18.53 JEOL ......................................................... 138 18.54 JPEG ......................................................... 138 18.55 JPEG 2000 ...................................................... 139 18.56 JPK .......................................................... 140 18.57 JPX .......................................................... 141 18.58 Khoros VIFF (Visualization Image File Format) Bitmap .............................. 141 18.59 Kodak BIP ...................................................... 142 18.60 Lambert Instruments FLIM ............................................. 143 18.61 Leica LCS LEI