1a614380325e080e72670e535c46597791e7ea68
20090721141349
1232611
jars/javac.jar
20090714155546
at-least
df831d146eca8e65f887f4704e706d1c9f867e7a
20080801134354
32775
4199e18036ba2020bdcbc733f603564f41cf9009
20090429190444
11814
92b2335d3a97549b633dbcc3c41381a90f2b924b
20090429190444
436656
jars/ant.jar
20090504010023
at-least
jars/batik.jar
20090506010300
at-least
jars/ant-launcher.jar
20090504010022
at-least
b1492f77c5c13e4f9dc05fe0ba9f95d6ec826660
20090429190444
1327716
jars/ant-launcher.jar
20090504010022
at-least
jars/batik.jar
20090506010300
at-least
dbab80ab5e11fb33328c7da88a849d0a19793ff5
20081218211215
8004326
jars/jacl.jar
20090506010254
at-least
jars/jython2.2.1/jython.jar
20090504010029
at-least
d21bc3c19ebc5b3924caff5f859e6c50071590c9
20080801134354
281694
efd0b4a7eaf55c0716fde3243ac45cb49fdd2606
20080801134354
69341
plugins/loci_tools.jar
20090722151044
at-least
3307d80c26d6b2657d0366edd562ace3bee8713b
20090429190853
482035
jars/batik.jar
20090506010300
at-least
368901ce572a723c0ae0e68f0563b2712a69fd5d
20080801134354
1341482
jars/junit-4.5.jar
20090506010300
at-least
jars/batik.jar
20090506010300
at-least
1b2240b7f87ce918bcebdcb6be2f0f75e5cf6d04
20090627012708
28709
jars/bsh-2.0b4.jar
20090504010023
at-least
jars/batik.jar
20090506010300
at-least
jars/jython2.2.1/jython.jar
20090504010029
at-least
ab4a901862f28e8bab9fe9ebd877ebea9ab6e08b
20080801134354
194151
plugins/Image_5D.jar
20090714155618
at-least
a88a4b46ddcdcf0312b0fe03b1900412bdb71873
20080801134354
1191495
jars/batik.jar
20090506010300
at-least
1d98f5251cb21553b4907228cd281e6b84d3a216
20081218211215
479044
253316728c4012a86fae361e7b7fcb0fab0f5c38
20080801134354
210930
2a328b6b63ebec85d369427875739304dc1cf2cb
20080801134354
1572799
jars/jai_codec.jar
20090504010024
at-least
d626e750c0076f3240b2675348efb6d633355b38
20090429190849
1041077
5000664ee8b54ad75a72da627ab7665ca422f10b
20080801134354
307734
d4ae386491403ffbf31335f27c0459f456161ac0
20080801134354
1291498
jars/jcommon-1.0.12.jar
20090504010024
at-least
jars/batik.jar
20090506010300
at-least
63e9057128a2096b3787c4c784a5b6dab862264d
20080801134354
1469651
jars/batik.jar
20090506010300
at-least
jars/jai_core.jar
20090504010024
at-least
jars/jai_codec.jar
20090504010024
at-least
jars/itext-1.3.jar
20090504010024
at-least
99a197bbc7b292264ffaf8b2d93dfe2252218f6f
20080801134354
4381607
108412260f226609c8161f6e831119f47e6d9380
20080801134354
756883
jars/batik.jar
20090506010300
at-least
bd25e435c97440c39a1edea79332016aad7f1091
20090612005019
206178
jars/jzlib-1.0.7.jar
20090504010029
at-least
8e9a4bd810c0d4c6cc42df2e974373c24f3b4372
20090429190853
211044
98e816fe8a5136547342df672bf6ff47cfd045d9
20080801134354
1941071
jars/jruby.jar
20090504010028
at-least
jars/ant.jar
20090504010023
at-least
a21f73a79260a9098df7eabf10982ab9ff2d9efe
20080801134354
48227
5cc5e4e537c2c5824beadcb03b7a1d6805e3a42f
20080801134354
431283
9624fa93cbf7720c01c7ff97c28b00747b700de3
20090429190902
6692
jars/Jama-1.0.2.jar
20090504010022
at-least
d2f6076c9bc8afa6f2d529828a6949340ae09e88
20090429190902
9789
jars/jzlib-1.0.7.jar
20090504010029
at-least
a6b17ee8970cf9a8d1986c9a9f89a37d6b4b225b
20090429190444
18858
12df5eeed674f9dc92b7c64c8f58cd59651b452c
20090713162954
Given an 8-bit grayscale image or stack, this plugin will analyze how the skeleton image is like. It would tag all pixels/voxels, counting all its junctions, triple points and branches and measures their average and maximum length. These information would be shown in a new window. An image showing the results of the analysis would also be displayed, with voxels having different colours according to their tag.
7534
57e92445bb3feda9d1ffe6e6d4a682b70d2d0ed9
20081015122324
Enables reading and saving of .img file format. Does this through menus File>Import>Analyze... and File>Save As>Analyze... respectively.
5506
e4181cd3a6cfb2364ef424acd2661d0ee93e25b4
20090429190901
1357
7e7a3543252f5916e5e70ea48916eec3082251f5
20090429190901
This plugin uses Thresholding, a simple method of image segmentation. Given a grayscale image, the plugin creates a binary image (Black and White) out of it. The plugin allows you to do either Global Threshold or Local Threshold. Here, global means histogram-derived. For local thresholding, the threshold is computed for each pixel according to the image characteristics within a window of a specified radius around it.
Details:
http://pacific.mpi-cbg.de/wiki/index.php/Auto_Threshold
http://pacific.mpi-cbg.de/wiki/index.php/Auto_Local_Threshold.
13744
16bbbd9df84c0de29f14784fda4f26d42b21e24b
20090429190854
1889
jars/bsh-2.0b4.jar
20090504010023
at-least
jars/fiji-scripting.jar
20090722192947
at-least
72d9597967ca05c9afd9ecba30728a90d7d22670
20090429190900
Aids a user in submitting a bug report to Bugzilla. User has to request an account at Pacific's Bugzilla Account Creation page in which the link would be provided by the Bug Submitter for the user to conveniently go to.
8609
f4a3d9514aac1a0b8731564b7b0adccf09694b4b
20090429190855
33701
jars/fiji-scripting.jar
20090722192947
at-least
6e2b780b0b70c89447c493c32e8b5ddeb003587b
20090429190854
7540
jars/fiji-scripting.jar
20090722192947
at-least
jars/clojure.jar
20090506010254
at-least
fb07498b2daab31e065eafda702f203fceef4413
20090603121121
17404
6f1f72445817f104f9d507e4cc38138f826e9746
20081015122324
This plugin displays histograms in three different channels (Red, Green and Blue) of a selected RGB image.
8034
abc9d5e1211a535b523bd8ca83ac3f9b08070773
20081015122325
72569
1a992dbc077ef84020d44a980c7992ba6c8edf3d
20090429190858
Simulates Colour Blindness for a selected image. There are different modes available to choose from, such as Protanopia, Deutanopia, Tritanopia, and others as well.
13859
35e88d42cbea67952727ac6c0ed07274fc0e7744
20090612005045
19995
jars/jsch-0.1.37.jar
20090714151221
at-least
30957bc0c0e1c2f6550841a13ff6dd09701cb55a
20090429190902
FlowJ is a collection of 2D optical flow algorithms. The plugin implements the main gradient-based optical flow techniques, such as Lucas and Kanade, Uras, Fleet and Jepson and Singh algorithms. It can measure and visualize the image flow (related to motion) in any open stack.
Links:
http://pacific.mpi-cbg.de/wiki/index.php/FlowJ
http://webscreen.ophth.uiowa.edu/bij/flowj.htm
241176
5ffe434d6901f67abb8811015552b03dcef32f63
20090604105207
16879
e3c2aca9e0404a89be29fb5785eb22392f2dbaee
20081218211221
2641
bd36c85b32a3d893cc7b7f5774a0d7cccd05322e
20090429190855
100649
jars/jpedalSTD.jar
20090504010025
at-least
jars/jzlib-1.0.7.jar
20090504010029
at-least
jars/itext-1.3.jar
20090504010024
at-least
jars/batik.jar
20090506010300
at-least
f108d740bd2a49a2b12e61c3149056ea16bf7119
20090429190857
The plugin extend image stacks to 5 dimensions: x, y, channel (color), slice (z), and frame (t). An Image5D has a "true" 5D format - Plugins working on stacks should usually work as expected on the currently displayed stack of an Image5D (Try z-projection to see what this means).
Image5Ds are displayed in a window with two scrollbars for slice and time below the image and a panel with controls to change the current channel and its color to the right of the image. A dropdown menu allows to change the display of the channels. Options are one channel in gray, one channel in color and an overlay of selected channels.
Links:
http://rsbweb.nih.gov/ij/plugins/image5d.html
100614
43bb3a7b79d1fc23958a7775f407fa9567c6f67f
20081015122325
72608
edbf88565a3d92c0ad28fc86c2839c34b66871c5
20090429190854
2681
jars/fiji-scripting.jar
20090722192947
at-least
jars/jruby.jar
20090504010028
at-least
16119f24746a02fe78d47bf9fa07dca96d03fafa
20090429190855
3308
jars/batik.jar
20090506010300
at-least
jars/fiji-scripting.jar
20090722192947
at-least
1bfa4e4d516e1496cf76e6e8b02c0d9db2166563
20090612193619
3982
jars/jython2.2.1/jython.jar
20090504010029
at-least
jars/fiji-scripting.jar
20090722192947
at-least
7f4ac83bb4c572cd21c416a011bef870a924f3f3
20090429190852
The LSM_Toolbox is a project aiming at the integration of common useful functions around the Carl Zeiss LSM510 .lsm file format, that should enhance usability of confocal lsm files kept in their native format, thus preserving all available metadata.
Links:
http://imagejdocu.tudor.lu/doku.php?id=plugin:inputoutput:lsmtoolbox:start
314424
756a2eafffb11114dc829c9d1cea777c8ed9c34d
20090429190900
7215
cf4237fdd463e67b4ca864f833d0ce5493f5d89f
20090429190857
10192
2bc2814e2471b6299a2111e0c408410b6d3e70f5
20090707154257
16840
202193ac1e64f640066b1e62f4fddcfa18951f4f
20090429190902
17006
0ab9e3b0886ae1aab0651865d98473295f2cc715
20090429190902
249
c2cd16e150ec6014c74e1e210522922096ddde78
20090429190901
3301
jars/fiji-scripting.jar
20090722192947
at-least
0f10f19bffda22d3b18bd936ab4f92f2c5fd1a53
20081218211221
Used for shape analysis. Given an 8-bit grayscale image or stack, the Skeletonize3D plugin will generate a thin version of the present shape (Skeleton image), making it equidistant to its boundaries. Some may regard this method as binary thinning. The shape is eroded iteratively until only the skeleton remains - It is performed symmetrically in order to guarantee the medial position of the skeleton lines and to preserve the connectedness of the object.
5912
41d82921719c38520d5472a3608b79394db1b7b0
20081015122324
35355
e58b7e0be52374fd085bfc202f098e7e181fe426
20090604105206
30003
240fab9dea2b358474349e2c89dfa715ac67a0f8
20090429190901
2937
c9a3332f9d9817aed8e1e06b87f7e62a793265f4
20090429190858
90445
plugins/loci_tools.jar
20090722151044
at-least
jars/edu_mines_jtk.jar
20090504010023
at-least
828d0b621fa15bb4a795e3b8a717871b72e33913
20090429190901
2280
ebecddff37b8e47da31f3f7e8d3c081d3b5ca76e
20090429190900
17544
91dffc21959c883588c46764eb49e62d982ced8c
20090627013736
TrakEM2 is a program to model from images, it is used for morphological data mining, three-dimensional modeling and image stitching, registration, editing and annotation. The plugin relies on segmentation - Partitioning a digital image into multiple segments for easier analysis. In the graphical interface of TrakEM2, each image and its elements can be analyzed, measured, quantified and transformed by other plugins in Fiji. It interacts with the 3D Viewer for visualization of image volumes and 3D meshes.
For more details on how to use it:
http://www.ini.uzh.ch/~acardona/trakem2_manual.html
http://www.ini.uzh.ch/~acardona/howto.html
1110662
jars/postgresql-8.2-506.jdbc3.jar
20090504010029
at-least
jars/batik.jar
20090506010300
at-least
plugins/loci_tools.jar
20090722151044
at-least
plugins/mpicbg_.jar
20090714155550
at-least
jars/Jama-1.0.2.jar
20090504010022
at-least
plugins/VIB_.jar
20090722193130
at-least
plugins/level_sets.jar
20090722193135
at-least
jars/jfreechart-1.0.9.jar
20090504010025
at-least
jars/edu_mines_jtk.jar
20090504010023
at-least
plugins/bUnwarpJ_.jar
20090714155550
at-least
d60cd1d7c1424f371dcb88460bc09b22e950ddb4
20090429190902
TransformJ is a package of ImageJ plugin classes for geometrical image transformation and manipulation, using simple as well as more complex and accurate interpolation techniques. The plugins can handle up to five-dimensional (5D) images.
Links: http://www.imagescience.org/meijering/software/transformj/
47976
jars/imagescience.jar
20090504010023
at-least
b309b43c769d8fc12c7047be85e33bba2aa8e62a
20090429190859
77054
c5c6c383c935b116d12199d30a3797538f3daa8f
20090721160531
Fiji's Tutorial Maker makes it easier for one to write tutorials to be published on the Wiki. It is able to take snapshots of the user's screen when instructed.
Help link:
http://pacific.mpi-cbg.de/wiki/index.php/How_to_make_a_new_tutorial
19839
6931a3f766ca75fa93b81f865e1adb8a93a06f97
20090513154207
1379965
jars/jzlib-1.0.7.jar
20090504010029
at-least
jars/junit-4.5.jar
20090506010300
at-least
jars/Jama-1.0.2.jar
20090504010022
at-least
jars/batik.jar
20090506010300
at-least
d6cf9638dc212f49fc3d2d4e99ca7aedc78956a2
20090429190902
22759
793c9e02bac38d5eb6647f1d85bc37ae9a86e8fa
20081218211221
The program View5D interactively displays of up to 5 dimensional volumetric datasets. Multi-dimensional data frequently arises in confocal microscopy and medical imaging applications.
Links:
http://www.nanoimaging.de/
http://pacific.mpi-cbg.de/wiki/index.php/View5D
117712
b8c3af50365b12b0beb010f1c35134cbd310341a
20081015122326
54309
be0c82083a917758fbfb8fa4f6734c786e0d1135
20090608232128
bUnwarpJ allows simultaneous and consistent registration of two images based on elastic deformations represented by B-splines. Registration is the transformation of one image into another. Here, one of the image would be elastically deformed in order to look as similar as possible to the other image. The plugin calculates an "inverse" transformation so that a pseudo-invertibility of the deformed image can be done. Thus two images are given as a result - The deformed versions of the two given images.
Links:
http://biocomp.cnb.uam.es/~iarganda/bUnwarpJ/index.html
http://pacific.mpi-cbg.de/wiki/index.php/BUnwarpJ
128032
659ad6a335b4947eef8758b1b0cf050779430b78
20081218211215
ij-ImageIO plugins add support for additional image file formats and their variants, including BMP, PNG, PNM, JPEG, TIFF. Added support provides for handling of compressed, tiled, 1bit, 16bit and 32bit images.
Links:
http://ij-plugins.sf.net/plugins/imageio
61670
jars/jai_codec.jar
20090504010024
at-least
8dd49f896fbdcd56fcd8ee91be4969bec732caa8
20090627012705
64940
bf4a838a22c4a05f0b56a5ca9096fa5ce54889a9
20090603155437
7518432
jars/batik.jar
20090506010300
at-least
jars/junit-4.5.jar
20090506010300
at-least
f382398d8871d25dac3c8617292e9e0c09ef531b
20090627012729
163097
jars/Jama-1.0.2.jar
20090504010022
at-least
b834726a38617dbf778898896fcd83ac9087624d
20090608171156
12068
plugins/mpicbg_.jar
20090714155550
at-least
plugins/bUnwarpJ_.jar
20090714155550
at-least
plugins/TrakEM2_.jar
20090722193106
at-least
4d7eaf239c033d305a464a06c3e64c68d096c7e1
20090429190855
23431
jars/edu_mines_jtk.jar
20090504010023
at-least
e6e0879f5d50afa8d0dd213b4b66e396a39a47b7
20081015121954
331716
e250f0c40b768e90ed7d3910d9869075f3e438cd
20081015121954
306814
jars/batik.jar
20090506010300
at-least
eea1390da8fac38763ed4c03f1acb3342b942717
20081015121954
173863
jars/ant.jar
20090504010023
at-least