Re-upping the postdoc search hoping for a new set of eyes:

https://apply.interfolio.com/139308

A full-time postdoctoral fellow position is available ASAP to contribute to a funded project examining olfactory sensory processing for social recognition in mice.

boldinglab.org

Hi all, we would like to introduce you to Spyglass (https://github.com/LorenFrankLab/spyglass) - our software framework for creating reproducible data analysis and data sharing for neuroscience research (spearheaded by Kyu Hyun Lee and myself, but really a group effort by the Frank lab).

Try it for yourself without any setup at https://spyglass.hhmi.2i2c.cloud/ thanks to support from @2i2c_org, @RapidScience, @HHMINEWS. Note that there might be a slight wait for things to load.

We all know how hard it is to keep track of all the parameters and code that go into processing neuroscience data. These choices fundamentally affect the outcomes of a paper, but we have few reliable ways of recording what those choices are.

One reason for this is neuroscience data is complex and writing good code that keeps track of these choices is hard. Researchers typically create ad-hoc pipelines to existing tools for themselves, but this is time consuming and potentially error prone.

We built Spyglass to make it easy for researchers to process and track their data. We make it possible for users to spikesort and curate their data using different spike sorters via @spikeinterface, track the pose of animals via @DeepLabCut, or more complex analyses like decoding

We make all this possible using the @NeurodataWB format. We believe that starting with data in NWB and keeping analyses within this format unlocks huge potential to take advantage of tools that rely on this standard. This makes it easy to share your data on @DANDIarchive.

We realized that simply processing data is not enough. You have to visualize your data to know processing worked, but there can be a lot of data with many data types. We make this easy using figurl - an interactive web-based visualization tool by Jeremy Magland (@FlatironInst).

For example, you can visualize spike sorting curation: https://figurl.org/f?v=gs://figurl/spikesortingview-10&d=sha1://1fa0b4a1663323b49b6f1934d79ca9f67779bda8&s=%7B%22initialSortingCuration%22:%22sha1://51b950cad7d97f26aaf807ba234e4b41ffade4ef%22,%22sortingCuration%22:%22gh://LorenFrankLab/sorting-curations/main/mcoulter/molly20220316_.nwb_r1_r2/15/curation.json%22%7D&label=molly20220316_.nwb_r1_r2_15_franklab_tetrode_hippocampus%20molly20220316_.nwb_r1_r2_15_franklab_tetrode_hippocampus_13f7a6a2_spikesorting

or visualize ripple detection: https://figurl.org/f?v=gs://figurl/spikesortingview-10&d=sha1://f94ea807087b446aa0ff7f1993fbafe7a9066f79&label=Ripple%20Detection&zone=franklab.default

or even visualize decoding of hippocampal mental representations: https://figurl.org/f?v=gs://figurl/spikesortingview-10&d=sha1://3990d47cfcfbe426fae203659479e55d7b08980f&label=j1620210710_clusterless_decode&zone=franklab.default

Finally, neuroscience research is becoming more collaborative within and across labs, but sharing data is still difficult. Spyglass makes it easy for you to share data by allowing collaborators to access the database and seamlessly download data via the cloud.

If you want to find out more, please read our preprint: https://www.biorxiv.org/content/10.1101/2024.01.25.577295v2

or view our documentation and tutorials: https://lorenfranklab.github.io/spyglass/latest/

We made a slack-like user group for 2p imaging in neuroscience, Diesel2p users, Cousa.

Just a place to share information, tips, discuss troubleshooting, techniques, etc.

If you want in, let me know. Or just try this link:
https://2p.ece.ucsb.edu/signup_user_complete/?id=6ozestbxr3ggt8j7et45pmuafr&md=link&sbr=sa

We're self-hosting it using Mattermost-- so the posts will stay indefinitely (no expiration data like free version of Slack). It's very much like Slack-- there are apps, and I use one on my phone, but on desktops and laptops I use the web interface, which works great.