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.

@albertcardona That's impressive. Are there connectomes already available as output of this massive collective effort?

@manlius Yes, a lot, but generated mostly with which is more purpose-built for .

An early reconstruction of a neural circuit done with was by Davi Bock et al. 2011 on the mouse visual cortex, "Network anatomy and in vivo physiology of visual cortical neurons"

Another one with was by Dan Bumbarger et al. 2013 "System-wide rewiring underlies behavioral differences in predatory and bacterial-feeding nematodes" where they compared with another nematode, pacificus that has the exact same amount of neurons but connected differently

Later ones with include:

The polychaete worm by @jekely 's group, "Whole-animal and cell-type complement of the three-segmented Platynereis dumerilii larva" Verazto et al. 2020

And all of ours in larva. See the server which hosts the of the whole central nervous system and lists all the neurons included in each published paper (currently 23), shared among the papers and all connecting to each other: l1em.catmaid.virtualflybrain.o)

The 24th will come soon, featuring the complete whole larval brain with ~2,500 neurons. It's under review.

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