Useful pieces from Twitter

Twitter used to be (and still is to some extent) a source of useful information for neuroscientists about technical details, clarifications of research findings and open discussions that cannot be obtained so easily otherwise. Here is a list of some these gems that have made it into my bookmarks, and I’m posting them here in order to archive their content at least to some detail. And yes, this list is mostly for my own reference, but it might be interesting for others as well.

Lab equipment

  1. Lior Golgher recommends to replace the expensive Conoptics Pockels cells with cheaper and better ones from Qubig, and he also makes suggestions for a fitting Pockels cell driver (A-303 or A-304).
  2. Munir Gunes Kutlu asks which camera to use to record mouse behavior compatible with posture tracking. Among the recommendations are Raspberry Pi cameras as the budget option (I have used those together with Sian Duss for pupillometry and was happy with it), the more expensive PointGrey Chameleon3 cameras; WhiteMatter cameras, where up to 15 cameras can be connected to a computer with a hub; the Basler cameras that are also used as a reliable option with few frame drops in the Helmchen lab; and the uEye XCP camera as a low-cost camera that is sufficiently good for academic purposes. It was mentioned that it is important to know beforehand whether single dropped frames are problematic or not. This is indeed important for simultaneous recording of longer chunks of behavior and neuronal activity in order to be able to synchronize two or more input streams.
  3. Tobias Rose and Jérôme Lecoq discuss where to buy cheap UV curing lights (often used for surgeries with mice to cure dental cement). Tobias bought his curing light from Aliexpress, Jérôme recommends one from McMaster-Carr and advices to use protective goggles in any case. Luke Sjulson adds that blue (not UV) curing lights are state of the art, and that they can be easily found by googling for “dental curing wand”. This made me remember a previous discussion involving Luke where curing lights and adhesive were also intensely discussed, where he recommended switching from Metabond to Optibond (both are used as the ‘the “luting” layer between bone and acrylic’).
  4. Guy Bouvier asks around for experience with iontophoresis pumps for AAV injection. I was completely unaware of this technique, which is apparently ideal for very controlled and small injections with less damage, the “gold standard for classical anterograde tracing” (according to Thanh Doan). Maximiliano Nigro seems experienced with this technique and recommends a specific precision pump.
  5. Matthijs Dorst asks about recommendations for oxygen concentrators vs. oxygen cylinders for isoflurane anesthesia stations for mouse surgeries. Oxygen concentrators seemed to work quite well, except for being rather noisy. Apart from the normal medical equipment brands (e.g., VetEquip), some reported using small fish tank pumps as a replacement for oxygen concentrators. It was mentioned that compressed air might work similarly well as compressed oxygen, but others noted that for very long procedures (>2h), mice started developing cataracts when using compressed air only. I also have learned some time ago that letting the mice inhale pure oxygen (without the isoflurane) after a surgery can improve and speed up the recovery from anesthesia.
  6. Based on some tweets (here and here), Andrey Andreev initiated a highly useful list of tips on how to set up a microscopy room (or any other lab room for a complicated data acquisition setup), including a lot of helpful links and considerations about lab infrastructure.
  7. On pre-Musk Twitter, Eleonore Duvelle used to initiate a lot of interesting discussions about rodent behavior and extracellular electrophysiology in hippocampus. She deleted these Twitter posts some time ago but is now very active on Mastodon. In addition, she has archived her Twitter threads on Github and has annotated some selected discussions in this Mastodon thread.

Software

  1. Joy A. Franco asks for tools to view z-stacks in 3D. Responses included the commercial and widely used Imaris or the free Imaris Viewer. Then, 3Dscript and ClearVolume as plugins for the open image analysis environment FIJI. Other free options included ChimeraX, AGAVE, FPBioimage. Also mentioned was Python-based napari. And, for very large (EM) datasets, there is Neuroglancer developed by Google. I wish I had the time to test all these options and compare them against each other!
  2. Maxime Beau highlights an interesting tool, the scientific Inkscape extension. Adobe Illustrator has been the best tool for vector graphic-based scientific illustrations, but Inkscape was always a good and free alternative. Affinity Designer is a newer and cheaper alternative which became more attractive when Adobe transformed to an annoying and very expensive cloud-based software a few years ago. In my opinion, all three tools are very useful, with Adobe Illustrator still being a bit better than the rest when you don’t consider the price tag. Importing PDFs generated with Python or in Matlab was, however, never easy. This extension is therefore a useful tool for any scientist using Inkscape for figure design.
  3. Matthijs Dorst asks which software/platform to use to quickly sketch out a custom imaging setup. Recommendations include gwoptics, which looks like a simple and straightforward-to-use library; more advanced, but maybe worth it for perfectionists, is Blender. A collection of example objects by Ryo Mizuta was highlighted, but there might be many more.

Other

  1. I’m no expert for sleep or sleep problems, but this thread brought up a lot of things and drugs that people apparently use to improve their sleep: amitriptyline; glycine + magnesium threonate; addition of taurine, ashwagandha, lavendar, valerian is considered; melatonin is recommended by some but not others; cannabis; antihistamines; tincture of hops; phosphatidylserine; a tidbit of morphine; trazadone; sodium axybate; gaboxadol; modafinil. I have not tried any and would not recommend anything, but I’d be curious to get all this weird stuff explained to me by an expert!
  2. Patrick Mineault asks for favorite podcasts on machine learning, neuroscience or general nerdy matters. Among the many recommendations are with a focus on neuro: Brain Inspired, the Huberman Lab Podcast, Brain Science Podcast, and the discontinued Unsupervised Thinking. With a focus on AI: Machine Learning Street Talk, TalkRL, Last Week in AI. And more broadly tuned podcasts: Sean Carrol’s Mindscape, Lex Friedman. The Twitter thread contains many more suggestions, but since I don’t like podcasts too much, I just picked some of them.

And many more threads that I forget here or that are too difficult to summarize.

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