Albert Cardona @albertcardona@qoto.org

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

Crete #neuroscience #Drosophila meeting is on for next summer. Spectacular #science in a wonderful setting.

#neuroscience #mentalhealth #science

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

... in which the authors show, using #vEM and #connectomics, that while the nematode #celegans 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.

URL: https://doi.org/10.1016/j.cub.2022.09.065

#readingpapers #science #neuroscience #development

The web-based open source software #CATMAID was devised as "google maps but for volumes". Documentation at https://catmaid.org and source code at https://github.com/catmaid/CATMAID/

Modern #CATMAID enables hundreds of #neuroscience 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 #connectome.

Running client-side on #javascript and server-side on #django #python #postgresql, 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: https://academic.oup.com/bioinformatics/article-abstract/25/15/1984/210794

See also public instances at the #VirtulaFlyBrain http://virtualflybrain.org/ particularly under "tools - CATMAID - hosted EM data such as this #Drosophila first instar larval volume of its complete nervous system https://l1em.catmaid.virtualflybrain.org/?pid=1&zp=108250&yp=82961.59999999999&xp=54210.799999999996&tool=tracingtool&sid0=1&s0=2.4999999999999996&help=true&layout=h(XY,%20%7B%20type:%20%22neuron-search%22,%20id:%20%22neuron-search-1%22,%20options:%20%7B%22annotation-name%22:%20%22papers%22%7D%7D,%200.6)

To fill in my profile tags, a thread:

#TrakEM2 is open source software mostly for #connectomics (but found uses well beyond), and provides the means for both manual and automatic montaging and aligning overlapping 2D image tiles (with #SIFT 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 #connectome from #vEM (volume electron microscopy).

#TrakEM2 paper at https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038011

Git repository at https://github.com/trakem2/

For 3D visualization, #TrakEM2 uses the 3D Viewer https://imagej.net/plugins/3d-viewer/

As software, #TrakEM2 runs as a plugin of #FijiSc https://fiji.sc/ and in fact motivated the creation of the #FijiSc software in the first place, to manage its many dependencies and therefore facilitate distribution to the broader #neuroscience community.

#TrakEM2 was founded in 2005, when terabyte-sized datasets were rare and considered large. The largest dataset that I've successfully managed with #TrakEM2 was about 16 TB. For larger datasets, see #CATMAID below.

Hello world! Here to (re)build a #neuroscience peer network.

#Drosophila #zebrafish #mouse #cephalopods

Also interested in #entomology #wasplove #nativebee #macrophotography and many more.

My website: https://albert.rierol.net

My #iNaturalist: https://www.inaturalist.org/lifelists/albertcardona?view=tree&details_view=observations