Discover and read the best of Twitter Threads about #napari
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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
biorxiv.org/content/10.110…
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biorxiv.org/content/10.110…
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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
protocols.io/view/whole-mou…
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protocols.io/view/whole-mou…
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By combining ExM with a new SPIM system based on technologies from electronics metrology, ExA-SPIM pushes past the volumetric imaging barrier 🚧 that constrains previous imaging approaches. (inspired by recent plot from @Daetwyler_St, @RetoPaul) #lightsheet #microscopy
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I used Matlab for image processing for years. Tried to switch to Python 10 years ago but too many tools were still missing. Tried again 5 years ago and haven't touched Matlab ever since! The combination scikit-image + @ProjectJupyter was a real game-changer! A few more things:
On top of the great classics scientific stack (#numpy, #scipy, #pandas, #matplotlib) there's an entire ecosystem of new tools to handle all sorts of complex problems. E.g. #napari to visualize and annotate multi-dimensional data. @dask_dev to handle very large images.
Complex ML tools for image denoising like content-aware image restoration #CARE (github.com/csbdeep/csbdeep) or point-scanning super-resolution #PSSR (github.com/BPHO-Salk/PSSR) which are documented as Jupyter notebooks that really work "out of the box".
