OnceMagicBrainEel @OnceMagicBrainEel@qoto.org

for open data to work, we have to have formats. this facilitates reuse.

to have formats to work, they have to be extremely easy to extend and use. this facilitates adoption.

for formats to be easy to extend, they have to be schema-driven: no new code for extensions. this facilitates accessibility.

for the formats to be easy to use, conversion should be a set of linear mappings from source data to schema properties. this facilitates interfaces.

for there to be no new code for format extensions and for conversion to be a set of linear mappings, the format tooling needs to be decoupled from the schema and from the storage representation. this facilitates maintenance.

I'm going to do some science outreach in my son's primary school, and I've received the most wonderful advice:

'when they start speaking, first ask them if it's a story or a question. if it's a story, make sure to cut them off early or they'll talk forever.'

*it works exactly the same with senior academics after presentations*

Make your next discovery using #Rastermap, a visualization method for large-scale neural data in #python. Paper now out: https://www.biorxiv.org/content/10.1101/2023.07.25.550571v1 (CLICK ON THE GIF) #neuroscience

Late #introduction:

I'm a junior group leader in neuroscience. Expertise in calcium imaging, microscopy, data analysis, ephys.

PhD with Rainer Friedrich on computations in adult zebrafish brains and postdoc with Fritjof Helmchen on hippocampal astrocytes. Now I'm interested in hippocampal plasticity.

Check out my blog: https://gcamp6f.com/a-blog-about-neurophysiology/
And Github: https://github.com/PTRRupprecht

I'm here for interesting papers, scientific discussions, methods questions, useful links.

Heading direction maps in the larval zebrafish? 😲
With an anatomical organisation? 🤯

Finally time for a paper tooth!
Check out the final version of our work from the Portugues lab with coauthors Hagar Lavian, You Wu, Fabian Svara and @vilim: https://doi.org/10.1038/s41593-023-01308-5
#neuroscience

While imaging (restrained) fish larvae, we observed a peculiar bump of activity propagating clockwise and anti-clockwise over a paired hindbrain nucleus. The bump was moving when the fish was turning left or right!

Welcome to all! ❤️​🐀​
Potential new followers: can we try something out?

- if you're a #Neuroscientist (of any status, yes, undergraduate students can be neuroscientists), could you answer with your neuro 'categories': Experimentalist, Computational, Philosopher, Fly, Human, Rodent, Whale, Tetrodes, Calcium imaging, fMRI, EEG, etc. This is so that I (and possibly others) can put you in a List! I'll share my lists once they have grown enough 😀​

- if you're not a Neuroscientist, this account will probably not follow you, but you are totally free to follow it, and also to tell us about you and any questions you might have about neuroscience!

- if you want to learn about neuroscience, I will try to post beginner-level explanations with the hashtag #NeuroForNewbies. Just an experiment...

One of the hardest lessons I’ve had to learn, but it changed everything.

@albertcardona The renderings of this data set by Amy Sterling on https://FlyWire.ai are beautiful. Others wanting to make their own videos can press one of the "3D viewer" buttons on that site to launch Neuroglancer, and then import its URL into neuVid. See the "Usage with Neuroglancer" section at https://github.com/connectome-neuprint/neuVid. Here's an example video showing the first 6 MBON pairs.

The connectome of the adult female fly brain, Drosophila melanogaster:

“Neuronal wiring diagram of an adult brain” by Dorkenwald et al. 2023 https://www.biorxiv.org/content/10.1101/2023.06.27.546656v1

A project that started with Davi Bock and Wei Lee developing the TEMCA for the mouse visual cortex in Clay Reid’s lab (Bock et al. 2011 https://www.nature.com/articles/nature09802), then Bock moving to #HHMIJanelia and developing the instrument much further to deliver the #FAFB volume (Zheng et al. 2018 https://www.sciencedirect.com/science/article/pii/S0092867418307876 ), and then the Seung, Murthy and Jefferis labs automatically re-registering, segmenting and annotating the whole volume via #FlyWire and more.

Extraordinary!

#Drosophila #connectomics #neuroscience #brain

A Laboratory technician position is available in our Animal Cognition and Neuroscience Laboratory at the Center for Mind/Brain Sciences (CIMeC), University of Trento.

Duration: 1 year, renewable to 3 years.

The application is in Italian, sufficient knowledge of the Italian language is required.

Deadline: 31/08/2023

https://lavoraconnoi.unitn.it/bando-pta/concorso/294-2023

On odour landscapes:

"How many compounds do natural odours typically contain? How often are those compounds shared across stimuli? What are the best statistical strategies for discrimination?"

"We quantitatively characterize the odour of 64 vertebrate species (mostly mammals), representing 29 families and 13 orders."

"Exploring natural odour landscapes: A case study with implications for human-biting insects" by Zung et al. 2023 https://www.biorxiv.org/content/10.1101/2023.05.08.539789v1

#neuroscience #olfaction #entomology #mosquitoes

It was a pleasure to host Loic Royer (CZI Biohub) for a Napari-ChatGPT Code Review @hhmijanelia

It was very exciting and I think watching it will give you a nice introduction to the project, but also how to get started using the #ChatGPT API for your own projects:

https://www.youtube.com/watch?v=JMo6Sn-L_j4

We are looking for a software engineer with background in mathematics and/or image alignment to work with us on reconstructing very large electron microscopy volumes:

https://hhmi.wd1.myworkdayjobs.com/en-US/External/job/Scientific-Computing-Software-Engineer_R-1972?locations=d48b8f09725a105a7c43ec0c1b9f4993

Best croissants in Paris. https://www.youtube.com/watch?v=wp84sRpM1Js

I am very happy to announce that our lab will soon move to the University of #Heidelberg to join the Centre for Organismal Studies (COS)
https://www.cos.uni-heidelberg.de/en
#COS

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