Albert Cardona<p>Now onto <a href="https://qoto.org/tags/FijiSc" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>FijiSc</span></a>: Fiji is a recursive acronym meaning "Fiji is just ImageJ" <a href="https://fji.sc" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="">fji.sc</span><span class="invisible"></span></a> (and the paper <a href="https://www.nature.com/articles/nmeth.2019" rel="nofollow noopener" target="_blank"><span class="invisible">https://www.</span><span class="">nature.com/articles/nmeth.2019</span><span class="invisible"></span></a> ) –and <a href="https://qoto.org/tags/ImageJ" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ImageJ</span></a> is a <a href="https://qoto.org/tags/java" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>java</span></a> open source software for image processing <a href="https://imagej.nih.gov/ij/index.html" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="">imagej.nih.gov/ij/index.html</span><span class="invisible"></span></a> written by Wayne Rasband from the <a href="https://qoto.org/tags/NIH" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>NIH</span></a> Research Branch.</p><p>An analogy: think of ImageJ as the kernel and Fiji as the rest of the operating system.</p><p><a href="https://qoto.org/tags/FijiSc" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>FijiSc</span></a> brings to <a href="https://qoto.org/tags/ImageJ" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ImageJ</span></a>:<br>(1) a package manager to install and update plugins, and that crucially enables reproducible science by exporting the whole set of plugins and libraries as an executable;<br>(2) a Script Editor <a href="https://imagej.net/scripting/script-editor" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="ellipsis">imagej.net/scripting/script-ed</span><span class="invisible">itor</span></a> supporting many languages (<a href="https://qoto.org/tags/python" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>python</span></a>, <a href="https://qoto.org/tags/groovy" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>groovy</span></a> <a href="https://qoto.org/tags/ruby" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ruby</span></a> <a href="https://qoto.org/tags/scala" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>scala</span></a> <a href="https://qoto.org/tags/clojure" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>clojure</span></a> and more), all with access to a huge collection of <a href="https://qoto.org/tags/JVM" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>JVM</span></a> libraries;<br>(3) huge amount of libraries such as <a href="https://qoto.org/tags/ImgLib2" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ImgLib2</span></a>, <a href="https://qoto.org/tags/JFreeChart" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>JFreeChart</span></a> for plotting, for GUIs, etc.</p><p>There are many, many plugins. A tiny sample: </p><p>Machine learning-based image segmentation:<br> - <a href="https://qoto.org/tags/LabKit" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>LabKit</span></a> <a href="https://imagej.net/plugins/labkit/" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="">imagej.net/plugins/labkit/</span><span class="invisible"></span></a><br> - <a href="https://qoto.org/tags/WEKA" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>WEKA</span></a> Trainable Segmentation <a href="https://imagej.net/plugins/tws/index" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="">imagej.net/plugins/tws/index</span><span class="invisible"></span></a></p><p>3D/4D/ND Visualization:<br> - 3D/4D Viewer <a href="https://qoto.org/tags/3DViewer" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>3DViewer</span></a> <a href="https://imagej.net/plugins/3d-viewer/index" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="ellipsis">imagej.net/plugins/3d-viewer/i</span><span class="invisible">ndex</span></a> with ray-tracing, orthoslices, volume rendering, and more<br> - <a href="https://qoto.org/tags/BigDataViewer" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>BigDataViewer</span></a> <a href="https://qoto.org/tags/BDV" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>BDV</span></a> <a href="https://imagej.net/plugins/bdv/index" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="">imagej.net/plugins/bdv/index</span><span class="invisible"></span></a> for interactively navigate N-dimensional image volumes larger than RAM</p><p>Image registration and serial section alignment:<br>- <a href="https://qoto.org/tags/BigStitcher" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>BigStitcher</span></a> for registering 3D/4D tiled datasets, with multiview deconvolution and more <a href="https://imagej.net/plugins/bigstitcher/index" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="ellipsis">imagej.net/plugins/bigstitcher</span><span class="invisible">/index</span></a><br> - <a href="https://qoto.org/tags/TrakEM2" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>TrakEM2</span></a> for montaging in 2D and alinging in 3D collections of serial sections, typically from <a href="https://qoto.org/tags/vEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>vEM</span></a> (volume electron microscopy) <a href="https://syn.mrc-lmb.cam.ac.uk/acardona/INI-2008-2011/trakem2.html" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="ellipsis">syn.mrc-lmb.cam.ac.uk/acardona</span><span class="invisible">/INI-2008-2011/trakem2.html</span></a><br> - <a href="https://qoto.org/tags/mpicbg" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>mpicbg</span></a> libraries for extracting <a href="https://qoto.org/tags/SIFT" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SIFT</span></a> and <a href="https://qoto.org/tags/MOPS" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MOPS</span></a> features, then finding feature correspondences and estimating rigid and elastic transformation models <a href="https://www.nature.com/articles/nmeth.2072" rel="nofollow noopener" target="_blank"><span class="invisible">https://www.</span><span class="">nature.com/articles/nmeth.2072</span><span class="invisible"></span></a><br> <br>Summarizing <a href="https://qoto.org/tags/FijiSc" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>FijiSc</span></a> is impossible. See the online forum where questions find answers by the hand of the broader community of users and developers <a href="https://forum.image.sc/" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="">forum.image.sc/</span><span class="invisible"></span></a></p>