Karsten Rodenacker

IDL goodies (?)

File I/O

• AIR3 Files
  are described in detail under Automated Image Registration and are widely used with MR, PET images/volumes, e.g. fMRI.
  • air_read.pro
  • air_write.pro
    are simple hacks to read and write AIR3 files, which consist of separate header and data files. The data are read in using readu. For further handling refer to idl home tips archive.
• Analyse 7.5 or AIR Files
  are described under Wikipedia Analyze and are widely used with MR, PET images/volumes, e.g. fMRI.
  • analyze75.zip
  are simple hacks to read and write AIR files version 7.5, which consist of separate header and data files. The data are read in using readu. The archive consists of several routines.
• Zeiss LSM Files
  are generated from Zeiss Laser Scanner Microscopes LSM 4xx and LSM 5xx. They are tiff similar images with privat headers.
  • ro_tiff_read.pro
    for tiff LSM 4xx
    is a hack using an older tiff_read from idl which returns some additional header information. The corresponding keyword is TCLSM. To interpret the returned data the function zeiss.pro can be called with these data and will return a structure. The description of this structure was found under Zeiss LSM 4xx TIFF topography and was originally provided by Zibigniew Iwinski.
  • lsm_read.pro
    for LSM 5xx files
    is an implementation following the description File Format Description - LSM 5xx Release 2.0, which I got by courtesy from Zibigniew Iwinski. This reference is a Word document of about 260 KB.
    The Zeiss private header can be accessed by the keyword ZEISS. It returns a structure named zeiss5 which is defined in zeiss5__define.pro. The function is not heavily tested. Planar configuration and multispectral images are not yet tested. I have to wait for example data. However thumnails, if there are any are read if keyword THUMBNAIL is set with a variable.
  • read_lsm.pro
    for LSM 5xx files
    is a wrapper for lsm_read.pro (see above) trying first to read the data with the IDL in-built read_tiff routine. Unluckily the re-arrangement part is not well tested caused by lack of enough lsm examples and personal time. For the re-arrangement option my routine ro_rgb2col.pro is necessary. Typically my old routine is used for images with two channels only. Such tiff images are not recognized as such by the idl query_tiff routine!
• bio-formats File reader
  as a trial of the IDL Javabridge I have partially implemented a reader using the OME at LOCI - Software - Bio-Formats library Java library. The ij_read_bio_formats interface routine is still in alpha state and tested under Mac OS X 6.4 with idl 7.1 and idl 8 . It can be used, some hints are given in the documentation.