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LungJ

    LungJ-logo.png

    Name

    LungJ

    Software

    ImageJ/Fiji

    Author

    Lasse Wollatz

    Maintainer

    Lasse Wollatz

    Source

    on GitHub

    Status

    stable, new

    Category

    Segmentation, Binary, Filtering, Image annotation

    Installation

    1) Help › Update…

    2) Manage update sites

    3) Add update site

    4) Name: LungJ

    5) URL: http://sites.imagej.net/LungJ/

    6) Close

    7) Help › Update…

    8) Restart Fiji/ ImageJ to apply changes.

    9) A new subdirectory called LungJ appears under Plugins.

    10) Future versions of LungJ will be updated together with the normal Fiji plugin updates.

    Function Documentation

    3D Blocks - Concatenate (Concatenate_3D)

    Plugins › LungJ › 3D Blocks › 3D Blocks - Concatenate

    Combines 3D blocks in a directory into a single image.

    3D Blocks - Create (Subdivide_3D)

    Plugins › LungJ › 3D Blocks › 3D Blocks - Create

    Divides a 3D image into 3D blocks and saves them into a directory along with header information in a txt file.

    3D Blocks - Halo Exchange (Halo_Exchange)

    Plugins › LungJ › 3D Blocks › 3D Blocks - Halo Exchange

    Exchanges the halos of a 3D Blocks image. This function can be applied between filters. Halos allow the avoidance of boundary errors/ inconsistencies.

    3D Blocks - Histogram (Block_Histogram)

    Plugins › LungJ › 3D Blocks › 3D Blocks - Histogram

    Opens the blocks of a 3D Blocks image, calculates all the relevant statistics and displays a histogram for all the blocks combined. Optionally saves the statistics to the properties directory.

    3D Blocks - Run Macro (Run_Macro_3D)

    Plugins › LungJ › 3D Blocks › 3D Blocks - Run Macro

    Runs a macro for each 3D block in a directory and saves the resulting image blocks to a new directory.

    Apply Binary Threshold (Create_Threshold_Mask)

    Plugins › LungJ › Tools › Apply Binary Threshold

    Creates a truly binary mask based on a fixed global threshold.

    Apply Mask (Apply_Mask)

    Plugins › LungJ › Tools › Apply Mask

    Applies a mask to an image, leaving the foreground as it is and replacing the background by black.

    Apply Weka Classifier (Apply_Weka_Classifier)

    Plugins › LungJ › Tools › Apply Weka Classifier

    Applies a Weka classifier based on the filename of an image and the filename of a classifier model. This implements the whole application process in a single function and does not require loading the original image into memory twice. This function is likely to suffer from updates to the weka-segmentation plug-in.

    Average ROIs Colour (Average_ROI_Colour)

    Plugins › LungJ › Other › Average ROIs Colour

    Finds the average value or RGB of active ROIs. The expected value range is overlaid on the histogram of the active image. Error calculations are based on

    Keith Dear, “An Online Text in Introductory Statistics.” (1999) University of Newcastle, Australia [online]. Was available at http://surfstat.newcastle.edu.au/ and

    Hans-Jürgen Andreß “Students T-Verteilung” (2001) [online]. Available at http://psydok.sulb.uni-saarland.de/volltexte/2004/268/html/surfstat/t.htm, last accessed: 22. July 2015.

    Colour by Segment (Colorize_)

    Plugins › LungJ › Other › Colour by Segment

    Combines a set of segmented images into a colour image.

    Compare Map to Mask (Compare_MapMask)

    Plugins › LungJ › Statistics › Compare Map to Mask

    Compares a probability map to a binary masks by combining them into a single colour-coded image. Agreed foreground is white and agreed background black. Foreground detected as background is blue and background detected as foreground red.

    Compare Masks (Compare_Masks)

    Plugins › LungJ › Statistics › Compare Masks

    Compares two binary masks by combining them into a single colour-coded image. Agreed foreground is white and agreed background black. Foreground detected as background is blue and background detected as foreground red.

    Convert Mask to STL (mask_to_stl)

    Plugins › LungJ › Other › Convert Mask to STL

    Takes a mask and converts and saves it as an STL file using Image Viewer 3D. This is useful if an image should be 3D printed.

    Create MCTV Tiles (Create_MCTV_Tiles)

    Plugins › MCTV › Create MCTV Tiles

    Creates jpg tiles and metadata file compatible with MCTV (code <doi:10.5258/SOTON/400332> , paper <doi:10.1109/eScience.2015.42>).

    Entropy

    Plugins › LungJ › Filter › Entropy

    Calls the Entropy filter from Trainable Segmentation/src/main/java/trainableSegmentation/filters/Entropy Filter.java

    Fill Holes Manual 3D (Fill_Holes_Manual_3D)

    Plugins › LungJ › Tools › Fill Holes Manual 3D

    Aims to fill holes of a mask. Ideal for filling a mask with many holes in the foreground but only one or few connected background(s).

    Gabor (Weka_Gabor)

    Plugins › LungJ › Filter › Gabor

    Applies the Gabor filter from Trainable Segmentation/src/main/java/trainableSegmentation/FeatureStack.java

    Invert Values (Invert_Values)

    Plugins › LungJ › Tools › Invert Values

    LungJ code for inverting the values in an image. This code changes the actual values and mirrors them around the centre between minimum and maximum. Values which exceed the minimum or maximum specified are being cut of at the boundary. The GUI looks up the minimum and maximum value in an image and suggests them as defaults.

    Label Hyperstack (Label_Hyperstack)

    Plugins › LungJ › Other › Label Hyperstack

    Consistently labels the slices of a hyperstack.

    Lipschitz

    Plugins › LungJ › Filter › Lipschitz

    Calls the Lipschitz filter from Trainable_Segmentation/src/main/java/trainableSegmentation/filters/Lipschitz_.java

    LungJ Settings (LungJ_Settings)

    Plugins › LungJ › LungJ Settings

    Allows to change standard settings for LungJ. This affects mainly 3D Blocks - Run Macro but also changes the default values for some other functions.

    Matrix Operation (Matrix_Operation)

    Plugins › LungJ › Filter › Matrix Operation

    Applies a 2D matrix onto an image. Can be used for GUI implementation of non standard matrix based filters.

    Membrane Projections (Weka_Membrane_Projections)

    Plugins › LungJ › Filter › Membrane Projections

    Applies the Membrane Projections filter from Trainable Segmentation/src/main/java/trainableSegmentation/FeatureStack.java

    Neighbors (Weka_Neighbors)

    Plugins › LungJ › Filter › Neighbors

    Applies the Neighbors filter from Trainable Segmentation/src/main/java/trainableSegmentation/FeatureStack.java

    Set Calibration (Set_Calibration)

    Plugins › LungJ › Other › Set Calibration

    Allows to set the Calibration of an image, similar to Image > Properties but with pixel value calibration function included.

    Stretch Histogram (Stretch_Histogram)

    Plugins › LungJ › Tools › Stretch Histogram

    Linearly stretch the values of an image.

    Test WEKA Filter (Test_WEKA_Filter)

    Plugins › LungJ › Filter › Test WEKA Filter

    Allows to compare WEKA filters visually. Note that the Gabor filter is currently not working.

    Publications

    Please note that LungJ, as well as other plug-ins available through Fiji, is based on a publication. If you use it successfully for your research please be so kind to cite our work:

    • TODO citation: , last1Wollatz; Wollatz, Lasse; Johnston, Steven J. (2016), LungJ v0.5.1, , ISSN