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#neuroscience

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Very excited that our whole-mouse-brain analysis pipeline - DELiVR - is published now at Nature Methods. With DELiVR, we built an open-source, easy-to-use pipeline for analyzing image stacks from cleared mouse brains.

Paper: nature.com/articles/s41592-024
Code: github.com/erturklab/delivr_cf
Docker containers, test dataset, handbook: discotechnologies.org/DELiVR/

#preprint_alert about #astrocytes, the roadies of the brain!

PhD student Imke Schuurmans and team have come up with a comprehensive one-step #differentiation protocol for turning human #iPSCs directly into functional Astrocytes, and how to co-culture them with induced human neurons on multi-electrode arrays for #electrophysiology.

From my new group (Nadif Kasri lab @radboudumc @DondersInst)

Preprint: biorxiv.org/content/10.1101/20

Imke's explainer: linkedin.com/posts/imke-schuur
#neuroscience #cellculture

We have now published a new and massively extended/reworked preprint of the whole-body #Platynereis larval #connectome with over 50 figures

biorxiv.org/content/10.1101/20

All the analyses, plots and figures should be reproducible in #rstats with the code provided:

zenodo.org/doi/10.5281/zenodo.

@zenodo_org

by querying our public #CATMAID database:

catmaid.jekelylab.ex.ac.uk

#neuroscience @biology #volumeEM
@biorxivpreprint

Call For Chapters

As Editor for the 2024 reference book, Ethics and Global Impacts of Human Enhancement Technologies, I invite you to submit formal chapter proposals to this forthcoming volume:

igi-global.com/publish/call-fo

This book is an extension of my 2014 book, Global Issues and Ethical Considerations in Human Enhancement Technologies: igi-global.com/book/global-iss

Thank you. Please share as compelled.

www.igi-global.com Call for Chapters: Ethics and Global Impacts of Human Enhancement Technologies | IGI Global
#BMI#BCI#biometrics

I guess instance migration is a good time for an #Introduction post. Hello lovely people, I'm here both as a scientific researcher and as a human being, and you can expect a range of genres of posts and interactions from me.

On the work side, I'm a computational scientist at Lawrence Berkeley National Laboratory in the field of biological X-ray crystallography, specifically at free electron lasers. It's a glorious interdisciplinary mess, and the description I give to non-scientists is that i use my degree in chemistry to write software to do math that models the physics of experiments that we're running to learn about biology.

For fellow structural biologists: I work on crystallography data reduction software for the steps between photons hitting the detector and a merged set of structure factors. I also support XFEL experiments, both on site and remotely, and assist in post-experiment data processing as needed. My PhD focused on using simultaneous XFEL crystallography and XES spectroscopy to probe the water splitting reaction in oxygenic photosynthesis. I did a postdoc in computational methods development for cryoEM, and I'm now back to XFEL crystallography but still in methods development.

For fellow software developers: all of our work is open source and mostly under the cctbx project/repo. It's mostly python with a bunch of C++ under the hood (including some low-level stuff redundant with scipy and numpy because those weren't around yet!), plus a user-facing wxPython GUI. More recently we've done a ton of work with GPU acceleration (using Kokkos, for NVIDIA, Intel and AMD architectures) and scaling up at three different national labs' supercomputing centers in anticipation of next-gen experimental capabilities. I derive too much joy from writing bash-sed-awk monstrosities on the occasions we need them to fix an urgent problem during an experiment, and I guess I'm most proud of the fact that I somewhat understand git.

As far as hobbies, the longest-standing one is probably #coffee, followed closely by #language (s) / #languageLearning and a love of #patterns and #symmetry in various contexts. I have too many different ways of making coffee (they have overrun my coffee cupboard), but my favorite remains the classic latte, and by now I can make a better latte than I can buy. I'm trying to refresh my #Japanese and learn #Dutch and #German simultaneously/comparatively, which of course is terrible for speed of learning, but fascinating. So far I've found #ASL the most challenging but also deeply satisfying -- I only have one semester under my belt but hope to take a lot more. I studied and continue to study all the #math and #science I possibly can. Right now I seem to be pretty engrossed in #electronics, #CAD, #3DPrinting, and just generally #DIY-ing/fixing/repairing things. Other active interests include #sewing, #reading, #cooking, #bike commuting, and #publicTransit. My journeys in #aikido and #pottery are on hold but I definitely want to pick them back up when I'm not already overcommitted. I'm casually interested in #neurophilosophy, #neuropsychology, #neurodivergence and #neuroscience. I've taken one course in neurophilosophy and can read literature in the rest, with effort.

On a personal note, I'm trans and nonbinary and very open about it -- I transitioned back when I had to explain what that meant. I've retired from some forms of community engagement and support but I'm very happy to answer any questions I can about the US legal and medical landscapes, available resources, policy and terminology best practices, or whatever you know you shouldn't ask [person in your life].

Finally, I spend a lot of time with my cat Rory (pictured), who is perfect and the most affectionate creature I have ever met. I promise to share photos of him from time to time.

#introduction I’m Susan Leemburg and I’m currently a post-doc in the Experimental Neurophysiology lab at Charles University’s Medical Faculty in Pilsen where I study how the rat hippocampus switches between different memory representations and how that relates to oscillations.
Before that, I worked on sleep stroke, motor learning and dopamine in Zurich.

Nice to e-meet you!
#neuroscience

#introduction

I fight for the users.

I love programming and thinking and talking about thinking. I have an education (BS, MS, PhD) focused on artificial intelligence and neuroscience.

I'm an advocate of the public academic pursuit of knowledge, the scientific process, peer review, and I see open source software and hardware as an essential part of the scientific process.

I see software user rights, including security and privacy, to be protected mainly by free open source software, specifically software with a copyleft license, i.e. GPL or Mozilla.

I see the democratizing effects of the Internet, including distributed journalism and social networking, to be largely the effect of the collaborative development of free and open source software.

I am interested in free and open source manufacturing, including open source 3D printers and CNC machines. I believe open source manufacturing will be important for distributed manufacturing, allowing local manufacturing and local labor.

I see worker-owned coops as the way to safely transition from a non-democratic authoritarian top-down power structure of a traditional corporation to a democratic work environment, where the workers own the company and elect the board of directors, transitioning to democracy in the workplace.

I believe that socialism is a regulatory response to capitalism.

I believe that laws, money, corporations, and government are social agreements, and I'm in favor of democratic social agreements.

I believe in the organized non-violent boycott as a way to control capitalists and change corrupt systems.

I am a pacifist. I am against violence. I am against citizens keeping guns in cities and towns with children. I am against war.

I try to eat plant-based / vegan foods to boycott the animal industry, to help with the climate crisis, to improve my health, to avoid animal cruelty, and to avoid the extinction of species of plants, animals and ecosystems.

I have been diagnosed with Retinitus Pigmentosa, which is a disease of progressive retinal degeneration. I am legally blind, although I have about 5-degrees of vision remaining in my fovea. I'm interested in researching and developing BCIs (Brain-Computer Interfaces), specifically BCIs that function as vision prostheses that may help with conditions like RP, or the more common degenerative retinal disease AMD (Age-related Macular Degeneration).

I enjoy playing computer games like Age of Empires and Rimworld. I used to program computer games when I was younger and would like to get back to it one day.

I love playing music, especially bass guitar. I've been listening to a lot of Rage Against the Machine and Enya recently.

I enjoy reading books, mostly non-fiction.

I enjoy studying religions. I've found a lot of value in Buddhism, and I meditate often daily.

Nina and I have recently had our first baby, a boy we call Tyoma.

I'm currently working at Apple on the Vision Pro headset team.

I'm sober.

@academicchatter

So I just learnt that J Physiol requires figures to be made with Biorender (biorender.com/), a VC backed subscription SaaS extend and extinguish of scientists drawing pictures!

Is this a thing now!? Complete privatisation of the publication workflow!?

Am I the only one enraged by this!? Pictures? We could have just made our own shared repository of useful graphics. Our own open source software. Uggghhh!

www.biorender.comBioRenderCreate Professional Science Figures in Minutes.

Today the peer-reviewed version of our preprint is out:

"The #connectome of an insect brain"
science.org/doi/10.1126/scienc

Congrats to co-first authors Michael Winding and Benjamin Pedigo, and to all our lab members and collaborators who made this work possible over the years. A journey that started over 10 years ago–and yet this is but a new beginning. So much more to come.

See my #tootprint on the preprint from back in the Autumn: mathstodon.xyz/@albertcardona/

The data is available both as supplements and directly via #CATMAID thanks to hosting by the #VirtualFlyBrain:
l1em.catmaid.virtualflybrain.o)

(The "Winding, Pedigo et al. 2023" annotation listing all included neurons will appear very soon in an upcoming update.)

#introduction because I may start using this as my main

I'm Lina - a #trans #nonbinary #neurodivergent #anarchist early-30s humanoid who enjoys nerdy interests and filthy friends (among others)

Currently working as a #software dev but strongly considering pursuing a PhD in #STS or #philosophyOfScience. I almost went for a #neuroscience PhD years ago but got frustrated by the state of the field & academia in general. Now I'm sick of software industry bullshit and thinking "might as well beat my head against a different wall for a while."

I'm also into everything #sound and #music, and have performed with bands, free improv sets, and theater productions. Also do some #fieldRecording, #audio software, #musicTheory, #psychoacoustics, etc etc. The weirder the sound, the better.

Lots more ofc, but this is already long. Nice to be here! 😄