fcollman

@stardazed0 @nc_znc I didn't really understand why they normalized by devices used... one big difference in technologies is how easy it is the parallelize across scopes.

Is there any experience curve data on connectomics progress? Something like this (from arxiv.org/abs/2103.14662) but tracking e.g. number of segmented synapses in published connectomics research over time

Excited to get started working on this! Will also aim to do 10 mm^3 at synaptic resolution across the basal ganglia, including NaC, VP, MD thalamus and VTA and the connections between, with segmentation from @zettaconnectome.

We posted our pre-print today describing how the Connectome Annotation Versioning Engine (CCAVE) supports analyzing and editing the worlds largest connectomics datasets biorxiv.org/cgi/content/sh…! @sdorkenw @csdashm @AllenInstitute @SebastianSeung!

@paulbohm @sdorkenw Huge variations from cell to cell, tens of thousands of different types. Different neurotransmitters abound. The complexity makes a LLM look simple in comparison.

@sdorkenw That's incredible! Are all the neurons and synapses functioning interchangeably, or is there considerable variation between them?

We are releasing a whole-brain connectome of the fruit fly, including ~130k annotated neurons and tens of millions of typed synapses! Explore the connectome: codex.flywire.ai Reconstruction paper: biorxiv.org/content/10.110… Annotation paper: biorxiv.org/content/10.110… 1/6

@BevilConway @eLife Journal editors for PNAS, Frontiers and SFN's eNeuro are all working scientists as well... to name a few.

@fcollman @eLife Others have high rejections BUT their editors are not publishing scientists so incentives differ. Sep powers! Eg: The FDA is not run by pharma executives with business before the agency. Is rejection rate the same for papers by eLife editors? Appearance of COI = bias against URMs

Science happens through theory, data, and publication. An important scientist-run journal, @eLife, recently made a major shift in how they handle publication. It’s caused major controversy. Here’s my attempt to explain why. #Science #research a 🧵 1/12

@BevilConway @eLife All other journals also have desk rejection, your argument introduces it as if it’s a unique feature of elife, plus your argument doesn’t make a clear case for an alternative that doesn’t already exist.

I tweet reluctantly. @eLife is run by scientists whose approval I desire (I can’t imagine my tweet pleases them). But my hesitation is itself evidence of the central challenge: science depends on the capriciousness of human decisions. Separation of powers is vital. 12/12

@AndrewHires Oh and if we can just add in some recordings from our phones and gps data we can save another 2 trillion and 200 years we spend on trying to record from neurons because brain machine interfaces will be unnesserary as we will predict all motor behaviors.

All the effort spent on brain preservation and a synaptic connectome, when the relevant embeddings are much more easily accessible. Just feed a generative model your gmail history and a few IG reels. Boom your brain is uploaded. Saved you $10B and 30 years of R & D.

Our scientists are using millimeter-scale #volumeEM to map the brain w/ single-synapse resolution. In a recent preprint, using data spanning millions of synapses across more than 1300 neurons, they reveal new organizing principles for cortical inhibition. biorxiv.org/content/10.110…

@cksalmo @HaniehFalahati We seem to find that the degree of this varies a lot by presynaptic cell type, a lot of thalamic axon synapses for example are almost fully surrounded by astrocyte, but others are less so. Perhaps firing rate and/or release probability related.

@HaniehFalahati These are great images bc they illustrate something confusing about PAPs - they very very rarely surround synapses with a fully connected ring structure. It looks like they do in these images, but you can see the breaks in the rings! Thanks for sharing :)

This #EM_Monday I will share some astrocyte hug. In these images, astrocytes (blue) surround the presynaptic boutons (green) and the dendritic spines( pink) that form a synapse.

@Aella_Girl @ClassOfProblem ```chunksize = 10 ** 6 for chunk in pd.read_csv(filename, chunksize=chunksize): process(chunk)```

@ClassOfProblem how do i only load part of it?

my data was too big for google sheets, so i installed and learned python. but now it's too big for my computer, python won't run it. off to buy a new computer i guess?

@timjarsky @TonyZador Bonus trick... zoom out a bit and drag the corner of the drawing to make it very large and then insert it and resize it in the google doc, will come out even higher resolution. If you put the caption in the drawing you'll need to use large font.

@TonyZador Make a google drawing that contains the image and caption. Then link to the drawing from the google doc.

what is the best way to insert an image & caption in a google doc? The way i am doing it renders the both kind of blurry. thx for any pointers

Happy to share my latest #neuro animation, a remix of previous #MICrONS videos, while I took some #SciArt license and had some fun, it remains quantitative. Possibly inspired by me having recently ridden Smuggler’s Run. A video🧵 1/4 #neuroscience #b3d

@HaniehFalahati Ah! Sorry I missed it. Love your EM mondays :)

@fcollman Yes what a great work! I really enjoyed reading it. Someone mentioned it last week and I tweeted about it

As a follow-up to last week's #EM_Monday, I wanted to know if there is anything inside nuclear membrane invaginations of neurons? It seems like the most common thing is clusters of vesicle like structures that are heterogenous in size. They are present in /1

@KennethHayworth But you ask so often and I respect you as scientist and colleague so I thought you deserved a response.

@KennethHayworth Given that I have these ethical issues with the idea and that its not why i'm doing what I do research in this area, elevating the profile of this idea is not really in my interest. Probably responding to this isn't either.

I’m sorry, but it is still really bugging me that we could ALL likely get to the future together (via quality brain preservation and far future mind uploading) if only the neuroscience community would start taking its own findings seriously and consider the implications. 1/6