Bio-Formats Documentation Release 5.1.2 The Open Microscopy Environment May 27, 2015 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 4 Bio-Formats versions 8 4.1 Version history .................................................... 8 II User Information 29 5 Using Bio-Formats with ImageJ and Fiji 30 5.1 ImageJ overview ................................................... 30 5.2 Fiji overview ..................................................... 32 5.3 Bio-Formats features in ImageJ and Fiji ....................................... 33 5.4 Installing Bio-Formats in ImageJ .......................................... 34 5.5 Using Bio-Formats to load images into ImageJ ................................... 36 5.6 Managing memory in ImageJ/Fiji using Bio-Formats ................................ 40 6 Command line tools 43 6.1 Command line tools introduction .......................................... 43 6.2 Displaying images and metadata ........................................... 45 6.3 Converting a file to different format ......................................... 46 6.4 Validating XML in an OME-TIFF .......................................... 48 6.5 Editing XML in an OME-TIFF ........................................... 49 6.6 List formats by domain ................................................ 49 6.7 List supported file formats .............................................. 50 6.8 Display file in ImageJ ................................................ 51 6.9 Format XML data .................................................. 51 6.10 Create a high-content screen for testing ....................................... 51 7 OMERO 53 8 Image server applications 54 8.1 BISQUE ....................................................... 54 8.2 OME Server ..................................................... 54 9 Libraries and scripting applications 57 9.1 FARSIGHT ...................................................... 57 9.2 i3dcore ........................................................ 57 9.3 ImgLib ........................................................ 58 9.4 ITK .......................................................... 58 9.5 Qu for MATLAB ................................................... 58 9.6 Subimager ...................................................... 59 i 10 Numerical data processing applications 60 10.1 IDL .......................................................... 60 10.2 KNIME ........................................................ 60 10.3 MATLAB ...................................................... 61 10.4 VisAD ........................................................ 62 11 Visualization and analysis applications 63 11.1 Bitplane Imaris .................................................... 63 11.2 CellProfiler ...................................................... 63 11.3 Comstat2 ....................................................... 64 11.4 Endrov ........................................................ 64 11.5 FocalPoint ...................................................... 65 11.6 Graphic Converter .................................................. 65 11.7 Icy .......................................................... 65 11.8 imago ......................................................... 65 11.9 Iqm .......................................................... 66 11.10 Macnification ..................................................... 66 11.11 MIPAV ........................................................ 66 11.12 Vaa3D ........................................................ 67 11.13 VisBio ........................................................ 67 11.14 XuvTools ....................................................... 68 III Developer Documentation 69 12 Introduction to Bio-Formats 71 12.1 Overview for developers ............................................... 71 12.2 Obtaining and building Bio-Formats ......................................... 72 12.3 Component overview ................................................. 74 12.4 Reading files ..................................................... 77 12.5 Writing files ..................................................... 79 13 Using Bio-Formats as a Java library 81 13.1 Using Bio-Formats as a Java library ......................................... 81 13.2 Exporting files using Bio-Formats .......................................... 82 13.3 Further details on exporting raw pixel data to OME-TIFF files ........................... 85 13.4 Converting files from FV1000 OIB/OIF to OME-TIFF ............................... 87 13.5 Using Bio-Formats in MATLAB ........................................... 88 13.6 Using Bio-Formats in Python ............................................ 94 13.7 Interfacing with Bio-Formats from non-Java code .................................. 94 14 Using Bio-Formats as a native C++ library 100 14.1 C++ overview .................................................... 100 14.2 C++ conversion details ................................................ 112 14.3 Tutorial ........................................................ 123 14.4 Environment ..................................................... 135 14.5 bf-test ......................................................... 136 14.6 bf-test info ...................................................... 136 14.7 bf-test view ...................................................... 138 15 Contributing to Bio-Formats 140 15.1 Testing code changes ................................................. 140 15.2 Public test data .................................................... 142 15.3 Generating test images ................................................ 145 15.4 Writing a new file format reader ........................................... 146 15.5 Bio-Formats service and dependency infrastructure ................................. 149 15.6 Code generation with xsd-fu ............................................. 151 15.7 Scripts for performing development tasks ...................................... 155 ii IV Formats 156 16 Dataset Structure Table 158 16.1 Flex Support ..................................................... 161 17 Supported Formats 162 17.1 3i SlideBook ..................................................... 167 17.2 Andor Bio-Imaging Division (ABD) TIFF ..................................... 168 17.3 AIM ......................................................... 169 17.4 Alicona 3D ...................................................... 170 17.5 Amersham Biosciences Gel ............................................. 170 17.6 Amira Mesh ..................................................... 171 17.7 Amnis FlowSight ................................................... 172 17.8 Analyze 7.5 ...................................................... 173 17.9 Animated PNG .................................................... 173 17.10 Aperio AFI ...................................................... 174 17.11 Aperio SVS TIFF ................................................... 175 17.12 Applied Precision CellWorX ............................................. 176 17.13 AVI (Audio Video Interleave) ............................................ 176 17.14 Axon Raw Format .................................................. 178 17.15 BD Pathway ..................................................... 178 17.16 Becker & Hickl SPCImage .............................................. 179 17.17 Bio-Rad Gel ..................................................... 180 17.18 Bio-Rad PIC ..................................................... 181 17.19 Bio-Rad SCN ..................................................... 182 17.20 Bitplane Imaris .................................................... 182 17.21 Bruker MRI ..................................................... 183 17.22 Burleigh ....................................................... 184 17.23 Canon DNG ..................................................... 185 17.24 CellH5 ........................................................ 186 17.25 Cellomics ....................................................... 186 17.26 cellSens VSI ..................................................... 187 17.27 CellVoyager ..................................................... 188 17.28 DeltaVision ...................................................... 188 17.29 DICOM ........................................................ 189 17.30 ECAT7 ........................................................ 191 17.31 EPS (Encapsulated PostScript) ............................................ 191 17.32 Evotec/PerkinElmer Opera Flex ........................................... 192 17.33 FEI .......................................................... 193 17.34 FEI TIFF ....................................................... 194 17.35 FITS (Flexible Image Transport System) ...................................... 194 17.36 Gatan Digital Micrograph .............................................. 195 17.37 Gatan Digital Micrograph 2 ............................................. 196 17.38 GIF (Graphics Interchange Format) ......................................... 197 17.39 Hamamatsu Aquacosmos NAF ............................................ 198 17.40 Hamamatsu HIS ................................................... 198 17.41 Hamamatsu ndpi ................................................... 199 17.42 Hamamatsu VMS .................................................. 200 17.43 Hitachi S-4800 ...................................................