ImageJ Plugins / News: Recent posts

ij-dcraw plugin opens raw images from digital cameras in ImageJ with a help of DCRaw tool. The dcraw is a C program created by David Coffin. Over 500 various cameras are supported, including Adobe DNG.

Improvements:

• dcraw binary updated to v.9.20

Bug fixes:

• Better support for file names with spaces (bug #30)

IJ Plugins Toolkit is a set of ImageJ plugins.

New:

• Plugin to apply k-means clustering to another image.

Developer visible:

• Dependent libraries updated to latest "full" release versions.

Requirements:

• Java 7 or better.

A stable version of Scala Console plugin is now available. ij-Scala enables editing and running Scala scripts from ImageJ. Scripts have full access to ImageJ API and API's of all installed ImageJ plugins.

The plugin installs under ImageJ menu: Plugins > Scripting > Scala Console

Download link: https://sourceforge.net/projects/ij-plugins/files/ij-scala/v.1.1.0/

Changes in v.1.1.0:

• Correct font in the Console.
• Add missing scroll pane to the output area.
• Update Scala to 2.9.3.
• Add ability to set scala script as an argument to the plugin (run(arg: String)).
• Upgrade RSyntaxArea library to v.2.0.6.

IJ Plugins Toolkit is a set of ImageJ plugins.

Improvements:

• Update ReadMe file that got quite out of date
• Fast filters modified to reproduce content of the image that is outside of the ROI to follow ImageJ convention.

Requirements:

• Java 7 or better.

New:

• k-means plugin now supports segmentation of 3D images.

Developer visible:

• k-means implementation renamed to KMeans2D. New class KMeans3D.

New:

• Plugins > Color > Measure Bands - measures color images and stacks writing results in a single row, rather than a separate row for each band or slice. Works on RGB images or gray level stacks.

Improvements:

• Stacks created by RGB to CIE Lab* and RGB to XYZ converters now have correct labels for each slice (name of the color band).
• Updated dependent libraries to recent versions.
• Add support for virtual stack to metaimage IO, based on patch provided by Eric Nodwell.
• Add help button to plugin options dialog
  -- Maximum Entropy Multi-Theshold plugin
  -- k-means Clustering plugin
  -- Region Growing plugin... read more

A stable version of Scala Console plugin is now available. ij-Scala enables editing and running Scala scripts from ImageJ. Scripts have full access to ImageJ API and API's of all installed ImageJ plugins.

The plugin installs under ImageJ menu:
Plugins > Scripting > Scala Console

Download link:
https://sourceforge.net/projects/ij-plugins/files/ij-scala/v.1.0.0/

I preview version of Scala Console plugin is available. ij-Scala enables editing and running Scala scripts from ImageJ. Scripts have full access to ImageJ API and API's of all installed ImageJ plugins.

The plugin installs under ImageJ menu:
Plugins > Scripting > Scala Console

Download link:
https://sourceforge.net/projects/ij-plugins/files/ij-scala/v.0.3.0/

ij-dcraw plugin opens raw images from digital cameras in ImageJ with a help of DCRaw tool. The dcraw is a C program created by David Coffin. Over 200 various raw formats are supported, including Adobe DNG.

New in this release:

• Many new options to control how the raw image is loaded
• Don't automatically brighten the images
• Output color space (raw, sRGB, Adobe, Wide, ProPhoto, XYZ)
• Document mode (no color, no interpolation)
• Document mode without scaling (totally raw)... read more

ij-Groovy enables editing and running Groovy scripts from ImageJ. Scripts have full access to ImageJ API and API's of all installed ImageJ plugins.

Download at: http://sourceforge.net/projects/ij-plugins/files/ij-groovy/v.1.0.0/

ij-plugins Toolkit v.1.5.2 at http://sourceforge.net/projects/ij-plugins/files/ij-plugins_toolkit/v.1.5.2/

Improved:

• RFE-3095953: MetaImage writer saved images in a single file (no header/raw separation)

Bug fixes:

• Bug-3097792: VTK Reader can handle images that spaces at the end of header lines.

ij-plugins Toolkit v.1.5.1 at http://sourceforge.net/projects/ij-plugins/files/ij-plugins_toolkit/v.1.5.1/

Improved:

• K-means Clustering: better cluster initlaiization using k-means++ algorithm
• K-means Clustering: option to send cluster centers to a result table
• MetaImage Reader supports images with local data
• MetaImage Reader: better support for working with macros
• Dependent libraries updated to latest versions

ij-plugins Toolkit v.1.5.0 at http://sourceforge.net/projects/ij-plugins/files/ij-plugins_toolkit/v.1.5.0/

New:

• Median 3D: correctly processes pixels along borders and executes faster
  than Fiji version.
• SRG: direct support for color and vector-valued images.

Improved:

• SRG Tool: Workarounds for bugs in RoiManager singleton.

ij-plugins Toolkit v.1.4.2 at http://sourceforge.net/projects/ij-plugins/files/ij-plugins_toolkit/v.1.4.2/

New:

• SRG: Add action icons.
• SRG: Send/load regions from ROI Manager.

Improved:

• Better Glass Pane implementation.
• Update RGB <-> Lab conversions to better match http://www.brucelindbloom.com

Developer visible:

• Add KMeans.closestCluster(final float[] x) to enable using result to cluster new image.

ij-plugins Toolkit v.1.4.1 at http://sourceforge.net/projects/ij-plugins/files/ij-plugins_toolkit/v.1.4.1/

New:

• SRG: Support for seeded region growing segmentation of 3D images.

Improved:

• SRG: Support non-consecutive seed numbers.
• SRG: Option to process single or all slices in the image (2D mode).
• SRG: Copy lookup table (LUT) from the seed image to the output segmented image.

Change:

• SRG API: seeds are specified as an image rather than lists of points.

Bug fixes:

• Set pixels plugin: correct behavior with stacks.

Developer visible:

• Use SVNAnt 1.3 for release number generation.

New Features:

• Seeded Region Growing (SRG) plugin

Improvements:

• Fast Median Filter plugin – added preview to options dialog.
• Code cleanup and removal of unused/obsolete classes.

Bug fixes:

• BUG-2687379: Division by zero in entropy threshold progress reporting.
  Pointed by Gabriel Landini.
• Correct potential numeric computation problem in maximum Entropy threshold
  pointed by Wilhelm Burger. EPSILON is made larger to avoid infinite result
  when dividing by values close to EPSILON.
• BUG-2690849: Multiband Difference Edge and Multiband Gradient Edge plugins
  were missing.

Other:

• Project code moved to Java 1.6.
• API for display of multi color overlays (OverlayCanvas)
• I/O Utilities API (IOUtils)

Improvements:

• Maximum Entropy Threshold plugin now supports 16 bit images.
• Several improvements to SRG algorithm (available through API).

Bug fixes:

• BUG-2037287: VectorProcessor: iterators bugs. Results in corrections
  to plugins that used VectorProcessor, like k-means and vector edge
  detector.

The 'ImageJ Plugins' project is a source of custom plugins for the Image/J software. Image/J is a public domain image processing and analysis program developed in Java (http://rsb.info.nih.gov/ij/).

Version 1.2 of the core ij-plugins is available.

Improvements:

• sRGB <-> XYZ <-> CIE Lab* conversion modified to use approach presented
  at http://www.brucelindbloom.com/.
• Improvements to maximum entropy threshold plugins.... read more

Source code of the project was migrated from CVS to SVN. The full commit history is preserved. It was not possible to convert CVS Branches and Tags, though that may not be of much importance.

The SVN repository has standard structure with trunk, branches, and tags. Most of the time you want to check out only trunk or one of its subdirectories. As URL of the repository use:
https://ij-plugins.svn.sourceforge.net/svnroot/ij-plugins/trunk... read more

The DCRaw Reader plugin opens raw image from over 200
digital cameras (Canon EOS 40D, Nikon D300, …).
The binaries and source code the plugin are available at:
http://ij-plugins.sourceforge.net/plugins/dcraw/
Note that reading of 48 bit RGB images requires ImageJ
v.1.39q or newer.

The DCRaw Reader plugin decodes images using DCRAW program
created by Dave Coffin. The source code for DCRAW and the
full list of supported cameras can be found at:
http://www.cybercom.net/~dcoffin/dcraw/... read more

The DCRaw Reader plugin opens raw image from over 200 digital cameras (Canon EOS 40D, Nikon D300, …). The binaries and source code the plugin are available at:
http://ij-plugins.sourceforge.net/plugins/dcraw/
Note that reading of 48 bit RGB images requires ImageJ v.1.35p or newer.

The DCRaw Reader plugin decodes images using DCRAW program created by Dave Coffin. The source code for DCRAW and the full list of supported cameras can be found at: http://www.cybercom.net/~dcoffin/dcraw/... read more

VTK binaries v.5.0.3 with Java wrappers for Windows available for download.

VTK binaries v.5.0.2 with Java wrappers for Windows available for download.

Version 1.1.1 of the core ij-plugins is available.

Bug fixes:

• BUG-1594780: Correct reading of COLOR_SCALARS: use GRAY8 when nValue==1, use RGB when nValue==3.

Improvements:

• Fast Median Filter Plugin: add support for RGB images.

Version 1.1 of the core ij-plugins is available.

Bug fixes:

• Correct spelling of PeronaMalikAnisotropicDiffusion* classes.

Improvements:

• VectorProcessor improvements.

• ProgressReporter - Change method names for access and update of current progress.

• Remove dependency on L2FProf library, use DialogUtils instead.

• Speedup computation of maximum entropy multi threshold by caching interval
  entropy computation (about 30x speedup for 3-threshold).... read more