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BioImageConvertor

This application is a command line image conversion utility. It can read and write many image formats, extract ROI and meta-data stored in images. Accepted image formats are: BioRad PIC, TIFF, Metamorph STK (uncompressed and LZW compressed), Fluoview TIFF, Carl Zeiss LSM 5, PSIA TIFF, Nanoscope II/III, JPEG, PNG, BMP, IBW, OME, RAW and video: QuickTime, AVI, MPEG1/2/4, Flash, etc.

Most functionality is provided by the libbioimage a C++ library for bio-image decoding and processing. Its source is tracked in this repos but can be extracted and used in other applications separately.

Release downloads

Binary releases are available in downloads section for most operating systems.

We also maintain a debian repository, check here how to add the repos to your debian-based system

Building

  • Ubuntu: install required packages and build with: make -j
  • Windows 64bit: Use Visual Studio 2015 to build msvc2013\imgcnv.sln
  • There's also a CMake based build system developed and maintained by Mario Emmenlauer which works for both Ubuntu and mingw under Windows.

Contributors

Contribute

Fork away and submit your patches! I'll review them as soon as possible and suggest changes if accepting directly is not possible

libbioimage

The application uses libbioimg for it's loading/saving and processing needs, although the library is larger and offers more to developers. The library is structured in several layers:

  1. image formats (image/video I/O)
  2. Format Manager for uniform access to all formats and
  3. Image processing API (image/stack/pyramid/histogram/lut/etc...)

Visit libioimage for more information on using libbioimage

Upcoming changes for v3

  1. Move to git and break the change history, we could preserve it but I feel we could start from scratch for v3 with reformatted code, etc
  2. Repository name will change and thus I need to update all webpages, etc to point to the new repos
  3. Reformat all files to 4 spaces tabulation
  4. Separate all third party repos into separate and downloadable packages
  5. Separate libbioimage and imgcnv into separate repos
  6. Add openslide and vips supported formats
  7. Modify metadata schema in splitting all channel info into per channel folders and all other necessary changes
  8. Document and test new CMAKE builds, possibly switching to them completely
  9. Make sure debian and windows packages are still buildable using gcc for debian and vc for windows

Updated