Bio-Formats Documentation Release 5.2.2 The Open Microscopy Environment September 12, 2016 CONTENTS I About Bio-Formats 2 1 Help 4 2 Bio-Formats versions 5 3 Why Java? 6 4 Bio-Formats metadata processing 7 4.1 Reporting a bug ................................................... 7 4.2 Version history .................................................... 8 II User Information 38 5 Using Bio-Formats with ImageJ and Fiji 39 5.1 ImageJ overview ................................................... 39 5.2 Fiji overview ..................................................... 41 5.3 Bio-Formats features in ImageJ and Fiji ....................................... 42 5.4 Installing Bio-Formats in ImageJ .......................................... 42 5.5 Using Bio-Formats to load images into ImageJ ................................... 44 5.6 Managing memory in ImageJ/Fiji using Bio-Formats ................................ 48 6 Command line tools 51 6.1 Command line tools introduction .......................................... 51 6.2 Displaying images and metadata ........................................... 52 6.3 Converting a file to different format ......................................... 54 6.4 Validating XML in an OME-TIFF .......................................... 56 6.5 Editing XML in an OME-TIFF ........................................... 57 6.6 List formats by domain ................................................ 58 6.7 List supported file formats .............................................. 58 6.8 Display file in ImageJ ................................................ 59 6.9 Format XML data .................................................. 59 6.10 Create a high-content screen for testing ....................................... 59 7 OMERO 61 8 Image server applications 62 8.1 BISQUE ....................................................... 62 8.2 OME Server ..................................................... 62 9 Libraries and scripting applications 65 9.1 FARSIGHT ...................................................... 65 9.2 i3dcore ........................................................ 65 9.3 ImgLib ........................................................ 65 9.4 ITK .......................................................... 66 9.5 Qu for MATLAB ................................................... 66 10 Numerical data processing applications 67 10.1 GNU Octave ..................................................... 67 i 10.2 IDL .......................................................... 68 10.3 KNIME ........................................................ 68 10.4 MATLAB ...................................................... 68 10.5 VisAD ........................................................ 69 11 Visualization and analysis applications 70 11.1 Bitplane Imaris .................................................... 70 11.2 CellProfiler ...................................................... 70 11.3 Comstat2 ....................................................... 71 11.4 Endrov ........................................................ 71 11.5 FocalPoint ...................................................... 71 11.6 Graphic Converter .................................................. 71 11.7 Icy .......................................................... 72 11.8 imago ......................................................... 72 11.9 Iqm .......................................................... 72 11.10 Macnification ..................................................... 72 11.11 Micro-Manager .................................................... 72 11.12 MIPAV ........................................................ 73 11.13 Vaa3D ........................................................ 74 11.14 VisBio ........................................................ 74 11.15 XuvTools ....................................................... 75 III Developer Documentation 76 12 Introduction to Bio-Formats 78 12.1 Overview for developers ............................................... 78 12.2 Obtaining and building Bio-Formats ......................................... 79 12.3 Component overview ................................................. 81 12.4 Reading files ..................................................... 84 12.5 Writing files ..................................................... 86 13 Using Bio-Formats as a Java library 87 13.1 Using Bio-Formats as a Java library ......................................... 87 13.2 Units of measurement ................................................ 91 13.3 Exporting files using Bio-Formats .......................................... 92 13.4 Further details on exporting raw pixel data to OME-TIFF files ........................... 94 13.5 Logging ........................................................ 96 13.6 Converting files from FV1000 OIB/OIF to OME-TIFF ............................... 96 13.7 Using Bio-Formats in MATLAB ........................................... 97 13.8 Using Bio-Formats in Python ............................................ 103 13.9 Interfacing with Bio-Formats from non-Java code .................................. 103 14 Using Bio-Formats as a native C++ library 104 15 Contributing to Bio-Formats 105 15.1 Code formatting ................................................... 105 15.2 Testing code changes ................................................. 105 15.3 Generating test images ................................................ 108 15.4 Writing a new file format reader ........................................... 111 15.5 Adding format/reader documentation pages ..................................... 115 15.6 Bio-Formats service and dependency infrastructure ................................. 116 15.7 Code generation with xsd-fu ............................................. 118 15.8 Scripts for performing development tasks ...................................... 121 IV Formats 122 16 Dataset Structure Table 124 16.1 Flex Support ..................................................... 127 ii 17 Supported Formats 129 17.1 3i SlideBook ..................................................... 134 17.2 Andor Bio-Imaging Division (ABD) TIFF ..................................... 135 17.3 AIM ......................................................... 136 17.4 Alicona 3D ...................................................... 136 17.5 Amersham Biosciences Gel ............................................. 137 17.6 Amira Mesh ..................................................... 138 17.7 Amnis FlowSight ................................................... 138 17.8 Analyze 7.5 ...................................................... 139 17.9 Animated PNG .................................................... 139 17.10 Aperio AFI ...................................................... 140 17.11 Aperio SVS TIFF ................................................... 141 17.12 Applied Precision CellWorX ............................................. 141 17.13 AVI (Audio Video Interleave) ............................................ 142 17.14 Axon Raw Format .................................................. 143 17.15 BD Pathway ..................................................... 144 17.16 Becker & Hickl SPC FIFO .............................................. 144 17.17 Becker & Hickl SPCImage .............................................. 145 17.18 Bio-Rad Gel ..................................................... 146 17.19 Bio-Rad PIC ..................................................... 146 17.20 Bio-Rad SCN ..................................................... 147 17.21 Bitplane Imaris .................................................... 148 17.22 Bruker MRI ..................................................... 149 17.23 Burleigh ....................................................... 149 17.24 Canon DNG ..................................................... 150 17.25 CellH5 ........................................................ 150 17.26 Cellomics ....................................................... 151 17.27 cellSens VSI ..................................................... 152 17.28 CellVoyager ..................................................... 152 17.29 DeltaVision ...................................................... 153 17.30 DICOM ........................................................ 154 17.31 ECAT7 ........................................................ 155 17.32 EPS (Encapsulated PostScript) ............................................ 155 17.33 Evotec/PerkinElmer Opera Flex ........................................... 156 17.34 FEI .......................................................... 157 17.35 FEI TIFF ....................................................... 157 17.36 FITS (Flexible Image Transport System) ...................................... 158 17.37 Gatan Digital Micrograph .............................................. 158 17.38 Gatan Digital Micrograph 2 ............................................. 159 17.39 GIF (Graphics Interchange Format) ......................................... 160 17.40 Hamamatsu Aquacosmos NAF ............................................ 160 17.41 Hamamatsu HIS ................................................... 161 17.42 Hamamatsu ndpi ................................................... 162 17.43 Hamamatsu VMS .................................................. 162 17.44 Hitachi S-4800 .................................................... 163 17.45 I2I .......................................................... 164 17.46 ICS (Image Cytometry Standard) .........................................