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ImageJ Macros & Plugins:

One common input data format for FluoRender is 8-bit multi-layer tiff, which can be converted from the manufacturer specific formats with ImageJ.
  1. Download ImageJ from ImageJ website:
    http://rsbweb.nih.gov/ij/download.html

  2. Launch ImageJ.

  3. From menu select "Edit->Options->Memory & Theread", then increase the memory amount. (Under 32-bit systems, maximum is 1450MB, and if a greater value is set, ImageJ fails to start; for 64-bit systems, higher settings are possible.)

An ImageJ macro converts various manufacturer specific confocal data formats to 8-bit multi-layer tiff
  1. In order to use the macro, install the "loci_tool" plugin for ImageJ first. The latest version of the plugin has problems running with the macro, an older version is here.
    Download:
    plugins.zip 5MB

  2. Copy the downloaded file into folder ImageJ/plugins/. Then restart ImageJ.

  3. Download the macro.
    The macro for format conversion of Zeiss, Leica and Olympus confocal microscopes:
    Save_8bit_multiCH.txt.zip

    Notes on files of the macro

  • [Save_8bit_multiCH.txt]
    This macro extracts channels from original confocal data file and generates 8-bit multi-layer tiff from each channel. The output files are in "TIFF_Files" folder, with the names of each 8-bit tiff file ended with "_B, _R, _G, _W".

  • [Save_8bit_multiCH1024px.txt]
    Similar functions to the macro above, this macro resamples the data from 1024px to 512px. Use this when graphics memory is insufficient.

    Attention: The macro fails to interpret the confocal data correctly if multiple samples are stored in a single file. Store each sample within one confocal data file.
    (The resulting 8-bit multi-layer file is usually mentioned as a volume dataset.)

How to run ImageJ macro
  1. Open the macro file with ImageJ, then from menu select "Macros->Run Macro".

  2. In the dialog box, select the folder where the input confocal data are. The macro reads all files in the folder, so keep only confocal data files in the folder.

    3. Attention: Spaces " " in file path or file name cause the macro read data files incorrectly. Use underscores "_" instead of spaces.

About the plugin
  • loci tools
    http://www.loci.wisc.edu/ome/formats.html
    The plugin allows us to read various formats of confocal files into ImageJ. But the latest version has problems with the macro. Use the older version provided above.