Philipp Schlegel @uni_matrix@qoto.org

This article nicely summarizes how NeuronBridge can be used to go from #connectome circuit to #fly strain by enabling access to large, open data sets. #drosophila #neuroscience #OpenScience
https://www.janelia.org/news/janelia-software-tools-power-fly-brain-research

If you download your Twitter archive it arrives wrapped as a static HTML page, which is not very useful for doing anything with, and worse: it requires the original account to be still active to do useful things like enlarge the images since they use t.co links.

So here's a Python script to convert a Twitter archive to markdown or other formats: https://github.com/timhutton/twitter-archive-parser

Now you can archive your tweets in any way you want.

Scientists move and scientific publishing follows:

@biorxivpreprint
@crossref
@ORCID_Org
@PLOSBiology
@eLife
@PNASNews
@nature
@sciencemagazine

Surely I’m missing many.
#academia #science #scicomm #publishing

@biorxivpreprint @crossref @ORCID_Org @PLOSBiology @eLife @PNASNews @nature @sciencemagazine

Found some more:

@arxiv_bio
@arxiv_cs
@arxiv_math
@arxiv_physics
@tmlrpub
@jmlr

#academia #science #scicomm #publishing

Are you in the U.S.? get out to vote today. Your vote matters, and could even help swing a race. In just one example, the election in our congressional district came down to *SIX VOTES* in the last election.

https://apnews.com/article/election-2020-donald-trump-iowa-mariannette-miller-meeks-elections-e3f235f217707a78fcec059f8e0b4ffa

What can you do with a #CATMAID server? Say, let's look at the #Drosophila (vinegar fly, often referred to as fruit fly) larval central nervous system, generously hosted by the #VirtualFlyBrain 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) or the #Platynereis (a marine annelid) server from the Jekely lab https://catmaid.jekelylab.ex.ac.uk/

First, directly interact by point-and-click: open widgets, find neurons by name or annotations, fire up a graph widget and rearrange neurons to make a neat synaptic connectivity diagram, or an adjacency matrix, or look at neuron anatomy in 3D. Most text–names, numbers–are clickable and filterable in some way, such as regular expressions.

Second, interact from other software. Head to r-catmaid https://natverse.org/rcatmaid/ (part of the #natverse suite by Philipp Schlegel @uni_matrix, Alex Bates and others) for an R-based solution from the Jefferis lab at the #MRCLMB. Includes tools such as #NBLAST for anatomical comparisons of neurons (see paper by Marta Costa et al. 2016 https://www.sciencedirect.com/science/article/pii/S0896627316302653 ).

If R is not your favourite, then how about #python: the #navis package, again by the prolific @uni_matrix, makes it trivial, and works also within #Blender too for fancy 3D renderings and animations. An earlier, simpler version was #catpy by @csdashm https://github.com/ceesem/catpy , who also has examples on access from #matlab.

Third, directly from a #psql prompt. As in, why not? #SQL is quite a straightforward language. Of course, you'll need privileged access to the server, so this one is only for insiders. Similarly privileged is from an #ipython prompt initialized via #django from the command line, with the entire server-side API at your disposal for queries.

Fourth, and one of my favourites: from the #javascript console in the browser itself. There are a handful of examples here https://github.com/catmaid/CATMAID/wiki/Scripting but the possibilities are huge. Key utilities are the "fetchSkeletons" macro-like javascript function https://github.com/catmaid/CATMAID/wiki/Scripting#count-the-number-of-presynaptic-sites-and-the-number-of-presynaptic-connectors-on-an-axon and the NeuronNameService.getInstance().getName(<skeleton_id>) function.

Notice every #CATMAID server has its /apis/, e.g., at https://l1em.catmaid.virtualflybrain.org/apis/ will list all GET or REST server access points. Reach to them as you please. See the documentation: https://catmaid.readthedocs.io/en/stable/api.html

In short: the data is there for you to reach out to, interactively or programmatically, and any fine mixture of the two as you see fit.