BioImageConvertor (imgcnv)

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.

• Using command line converter

• Supported formats

• Version change log

Release downloads

 Binary and source release downloads

 Our debian repository for imgcnv

Contributors

• Mario Emmenlauer,  XuvTools - the "eXtend yoUr View" Toolkit
• Michel Boudinot, INAF - CNRS

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Development

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

TODO

#6

-info call should not read the first page, try tooptimize

#7

pass file name to magic number test, to desimbiguate sometimes using the extension

#15

abnormal times for thumbnail generation with maximum intensity projection

#28

update file names to unicode throughout the library

#29

major renaming and namespaces for libbioimage

#32

Support Andor images + stage coordinates

#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

#48

parallelize most channel operations with threads

#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

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...)

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