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 🧵 (2/n)

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 🧵 (3/n)

The lens 🔎 at the heart of ExA-SPIM provides NA = 0.305 (1 µm resolution) over an incredible 16.8 mm FOV. This is paired with a 151 megapixel CMOS camera 📷, far exceeding the capabilities of traditional technologies. They are big! #bigscience 🧵 (4/n)

We modified the optical system to achieve an aberration free working distance of 35 mm (!) into liquid 💧 mounting media. #deepimaging #highresolution 🧵 (5/n)

ExA-SPIM can image an incredible 200 x 52 x 35 mm3 volume, with 1 µm near-isotropic resolution over a 10.6 x 8.0 mm field of view. - at up to a 1 gigavoxels/sec 💨! #largevolume 🧵 (6/n)

ExA-SPIM can therefore image an entire 3X expanded 🐁 mouse brain - with 300 nm effective resolution - in only 15 tiles - and in less than one day. This produces ~100 TB of raw data! #highspeed 🧵 (7/n)

With no sectioning and few tiles, these volumes are easily stitched and merged for downstream analysis, including tracing ✏️ and reconstruction of individual neurons across the mouse brain. #neuralcircuits #hortacloud 🧵 (8/n)

ExA-SPIM is also a charm for larger brains 🧠. We imaged a 1x1x1.5 cm block of macaque brain. ExA-SPIM reveals brightly ⚡ labeled cortico-spinal tract neurons, their dendritic arbors, and incredibly dense dendritic spines as well as descending axons. #connectomics 🧵 (9/n)

ExA-SPIM required new 🐍 acquisition software for controlling the microscope. Data is streamed using ACQUIRE, a new multi-camera 📸 streaming software, led by @ChanZuckerberg in collaboration with our team. #acquisitionsoftware #napari 🧵 (10/n)

Using a combination of high-speed networking, fast on-premises storage, and real-time compression, our current imaging pipeline enables an imaging throughput to cloud ☁️ storage of >100 TB per day, using commodity hardware. #cloudcomputing 🧵 (11/n)

This collaboration was only possible at @AllenInstitute for Neural Dynamics, and represents the hard work of many team members! Including @vcj029, @svoboda314, @dyfbrain, @rclayreid, @sejdevries, @poofjunior, @nclack, @kjcao, @KalmbachsCortex, and many others. #teamscience