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