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Wonderful project @JoachimFuchs Do you have any data yet on variability in the self-assembly of the brain?


Joachim Fuchs  
Hi everyone at fediscience #introductions I'm a postdoc in Berlin, my background is cell biology & biochemistry. I use this now to (try to) un...

Crete meeting is on for next summer. Spectacular in a wonderful setting.

Kristin Branson  
The Crete Fly Neuro conference is my absolute favorite. Drosophila neurobiologists, save the date: May 28-June 2023, 2023 RT
Matteo Carandini  
"Neuroscientists accept foundationally that the brain represents every distinct thought, feeling, and behavior as some sort of neural ripple: a sad...

"Post-embryonic remodeling of the C. elegans motor circuit" by Ben Mulcahy et al. 2022 (Mei Zhen's lab

... in which the authors show, using and , that while the nematode nervous system grows from ~200 neurons in the hatchling to ~300 in the adult, the addition of new neurons doesn't disrupt existing motor function, but new circuits are formed that endow the animal with new behaviors such as bending.

Interestingly, in the course of larval maturation one neuron type inverts its polarity: what was the dendrite becomes the axon, and viceversa. And this is accomplished not with retraction and regrowth of the arbor, but rather, by flipping the synapses in situ.


The web-based open source software was devised as "google maps but for volumes". Documentation at and source code at

Modern enables hundreds of researchers world wide to collaboratively map neuronal circuits in large datasets, e.g., 100 TB or larger, limited only by bandwidth and server-side storage. The goal: to map and analyse a whole brain .

Running client-side on and server-side on , it's a pleasure to use–if I may say so–and easy to hack on to extend its functionality with further widgets.

The first minimally viable product was produced in 2007 by Stephan Saalfeld (what we now refer to, dearly, as "Ice Age CATMAID), who demonstrated to us all that the web, and javascript, where the way to go for distributed, collaborative annotation of large datasets accessed piece-wise. See the original paper:

See also public instances at the particularly under "tools - CATMAID - hosted EM data such as this first instar larval volume of its complete nervous system l1em.catmaid.virtualflybrain.o)

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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.

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