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BioImageConvertor (imgcnv)

This repository has been moved to bitbucket!

This is the developer web site for recording documentation, and bug reports. If you're looking for user-side information check out our main web page.

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.

Release downloads

Binary and source release downloads

Our debian repository for imgcnv here is how to add the repos into your debian system

Contributors


Development

If you simply want to browse the source code, please use our Online Source Browser

TODO

#33
Support stage coordinates from Zeiss LSM7 files
#34
Imaris HDF5 support using Mario's open source reader
#35
java-based LOCI Bio-Formats support using Mario's open source reader for c++
#36
test ZVI 4D files from Mario
#41
create tests for content-based overlap detection
#42
create tests for histogram storage and retrieval
#46
in overlap determination, compute transforms between near images and then estimate overlap with the previous key frame
#49
incorrect ome-tiff geometry stored if converting an ome-tiff to another ome-tiff and sampling pages
#50
create tests for channels in Zeiss LSM
#51
Some metadata elements are lost in conversions
#54
2 channels erroneously mapped into red for fluoview tiff
#62
zvi to jpx
#64
Add histogram support for brightness, contrast, levels
#66
Add DICOM-145 Whole slide image support WG26
#68
support WebP format
#71
support DICOM-145 tile decoding
#72
Add proper modification of histogram for all ops changing it, i.e. levels, brightness...

Getting the source

We are using Mercurial for our source control system, so it should be installed before proceeding. You can get a read-only copy of imgcnv with the following command:

   hg clone http://biodev.ece.ucsb.edu/hg/imgcnv

If you plan on submitting patches directly to our repository, You must be an enabled user. You can become a user by sending mail to kris@….

In a nut shell, developers must are able access the source using ssh. In order to access the code you must provide me with your id_rsa.pub or id_dsa.pub, which you can find or generate using ssh-keygen. The default location will be in your ~/.ssh/id_rsa.pub

Once you are enabled you can get copy with

hg clone ssh://hg@biodev.ece.ucsb.edu/imgcnv

Making a release

Once all updates to the source are done and all tests performed and you are ready to release, follow these procedures:

  • Tag the repository version:
    hg tag Release-X.XX -m "Release X.XX"
    hg push
    
  • Update the Version change log wiki page
  • Compile and upload all binaries into the Trac Uploader
  • Compile and upload debian packages

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 libioimg for more information on using libbioimage

Last modified 18 months ago Last modified on Jun 8, 2016 12:37:20 PM