BioImageXD

BioImageXD 1.0RC3 to be released by the end of the week 15

BioImageXD 1.0RC3 will be released by the end of the week 15. Most important improvement will be a fix to bug 3498498 that complicates of processing of time series data in Procedure list task. Release will also include smaller bug fixes and improvements.

Wiki under construction

BioImageXD Wiki is currently unavailable. We hope to get updated Wiki running on 21st of December, 2011. When new Wiki is running, we'll start updating and adding new information to it, including the latest instructions for developers and users. We plan to use new Wiki considerably more than we used to including basic information, but also typical use cases to solve image analysis problems in BioImageXD.

Update (4th of January, 2012): Because of technical issues in our web server, Wiki will be unavailable for a while. We hope to get it back online as soon as possible.

BioImageXD 1.0 Release Candidate 2 released

We are happy to release BioImageXD 1.0 Release Candidate 2. There are some important improvements and many bugs are fixed after the release of the first release candidate. Packages for 32/64-bit Windows, 64-bit Linux and 64-bit OSX 10.6/10.7 are available at the Download page and in SourceForge. Download page includes installation instructions for all packages.

Even though BioImageXD is already on release candidate phase, we wanted to include a few new functionalities to be in the BioImageXD 1.0 package. These are:

• OME-TIFF reader and writer
• Caching of result data in Procedure list task (no re-processing needed anymore when visualization mode or channels are changed).
• Geodesic active contours filter
• 4D particle simulation filter
• Support for RGB TIFF stacks (missing support caused lots of traffic to our bug mailing list after release of release candidate 1)
• New instructions and structure in Import dialog to ease usage.

BioImageXD 1.0 Release Candidate 1 released

BioImageXD 1.0RC1 is the first release candidate of official version 1.0 release. This means that all functionality is final, but there might still be some bugs that we will fix before releasing version 1.0. If you find any bugs, please report those to our bug tracker.

We provide packages for 32 and 64-bit Windows (Xp, Vista, 7), 64-bit Linux and 64-bit Mac OSX 10.6. Windows packages are installers for automatic installation. To use Linux or Mac OSX package, first extract package and then read either readme_linux.txt or readme_osx.txt for instructions to set LD_LIBRARY_PATH or DYLD_LIBRARY_PATH. Also Linux package needs Python 2.6 and wxPython 2.8.x installed where as Mac OSX package needs Python 2.7. Mac OSX 10.6 version might include more bugs than other packages. We plan to improve Mac version and also provide package for 10.7 (Lion) in coming months.

Changes since previous release (r1537):

• Versions for 64-bit Windows, 64-bit Linux and 64-bit Mac OSX 10.6.
• Getting started guide included in the software.
• Enhanced GUI functionality including descriptions and input/output image types for all filters.
• Support for 8/12/16/32 grayscale images, RGB images and 32/64-bit label images.
• MRC file format reader.
• Support for multipage TIFF files.
• Improved memory handling.
• Many fixed bugs.
• Updated libraries: VTK 5.6.1 and ITK 3.20.
• 3D visualization of multiple channels without grouping.
• Filters for deconvolution and mathematical generation of PSF.
• Possibility for FRAP analysis.
• Many new registrations filters.
• Fourier and Inverse Fourier transforms. Low and high pass filters.
• Filter to remove background gradient from images.
• Difference of Gaussians filter for improved spot detection.
• Possibility to filter objects by size, border connection and roundness.

New filters in procedure list task (21):

• Mean (smoothing)
• PSF generation (deconvolution)
• Iterative deconvolution (deconvolution)
• Difference of Gaussians (spot detection)
• Binary thinning (3D skeleton of binary data)
• FFT, Inverse FFT, Butterworth low pass, Butterworth high pass, Ideal low pass, Ideal high pass
• Non-uniform illumination correction (to remove background gradient)
• Filter objects (remove labeled objects)
• FRAP analysis
• Versor rigid registration, Rigid registration 2D, Deformable registration, Translation registration 2D, Slices translation registration
• Combine images (compute single image from two)
• Extract components (extract components of RGB image)