To fill in my profile tags, a thread:

is open source software mostly for (but found uses well beyond), and provides the means for both manual and automatic montaging and aligning overlapping 2D image tiles (with features and rigid or elastic transformation models), and then reconstructing with mostly manual means–by painting with a digital brush–the volumes of structures of interest, as well as trace the branched arbors of e.g., neurons and annotate their synapses, therefore mapping a from (volume electron microscopy).

paper at

Git repository at

For 3D visualization, uses the 3D Viewer

As software, runs as a plugin of and in fact motivated the creation of the software in the first place, to manage its many dependencies and therefore facilitate distribution to the broader community.

was founded in 2005, when terabyte-sized datasets were rare and considered large. The largest dataset that I've successfully managed with was about 16 TB. For larger datasets, see below.

Now onto : Fiji is a recursive acronym meaning "Fiji is just ImageJ" (and the paper ) –and is a open source software for image processing written by Wayne Rasband from the Research Branch.

An analogy: think of ImageJ as the kernel and Fiji as the rest of the operating system.

brings to :
(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;
(2) a Script Editor supporting many languages (, and more), all with access to a huge collection of libraries;
(3) huge amount of libraries such as , for plotting, for GUIs, etc.

There are many, many plugins. A tiny sample:

Machine learning-based image segmentation:
- Trainable Segmentation

3D/4D/ND Visualization:
- 3D/4D Viewer with ray-tracing, orthoslices, volume rendering, and more
- for interactively navigate N-dimensional image volumes larger than RAM

Image registration and serial section alignment:
- for registering 3D/4D tiled datasets, with multiview deconvolution and more
- for montaging in 2D and alinging in 3D collections of serial sections, typically from (volume electron microscopy)
- libraries for extracting and features, then finding feature correspondences and estimating rigid and elastic transformation models

Summarizing is impossible. See the online forum where questions find answers by the hand of the broader community of users and developers

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For an introduction to from the comfort of (or rather, 2.7), see my online tutorial, walking you through image processing concepts with working code that you can copy-paste into the Script Editor, which has code autocompletion to facilitate class and method discovery across the many libraries:

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