Developing hardware + software tools for large-scale imaging @AllenInstitute for Neural Dynamics. also @adamkglaser@fediscience.org
Jun 12, 2023 • 12 tweets • 12 min read
How do you image the large and the small at the same time? We developed new 🔬 technology to image centimeter-scale specimens - including whole mouse brains 🧠 - with diffraction-limited resolution and without sectioning. #mesoscale#imaging
🧵 (1/n)
ExA-SPIM is a technology based on innovations in (1) tissue processing and (2) large-scale microscopy 🔬. Our team developed new methods for expansion for microscopy (ExM) of large tissue volumes. #teamscience#expansionmicroscopy
Thoughts on fastest ways to down-scale ND matrices by factor of 2 in Python? [0::2] is blazing fast but throws away information. skimage.transform.downscale_local_mean() is great - but quite a bit slower.
Great follow up article from what @DataNerdery shared here: towardsdatascience.com/countless-3d-v…. Has some great comparisons on throughput of different approaches (including those already mentioned).
