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Rob Campbell

@raacampbell.com

379 followers 178 following 126 posts

Advanced Microscopy Facility Manager Sainsbury Wellcome Centre, UCL swcmicroscopy.com

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Rob Campbell @raacampbell.com · 04/10/2026

Here's a short clip of the acquisition software in action, tile-scanning a four-sample block. Terminal window at top-right is from the stitching & pre-processing PC. BrainSaw has contributed to 35 papers so far. Learn more at: swcmicroscopy.com/brainsaw

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Rob Campbell @raacampbell.com · 04/10/2026

BakingTray plugs into ScanImage via its API. ScanImage handles image acquisition; BakingTray handles the logistics of serial sectioning: tiling, slicing, and finding the tissue. The software is modular and supports a range of hardware and configurations. Docs: bakingtray.swcmicroscopy.com

Screenshot of BakingTray (dark windows) running alongside ScanImage (light grey windows), which it controls via ScanImage's API. Header boxes list the division of labour. ScanImage: image acquisition, laser power and PMT control, channel selection. BakingTray: acquisition resolution, laser wavelength tuning and monitoring, tile scanning, slicing and sample detection. The large acquisition window (bottom right) shows a four-brain acquisition, with the current section nearly finished on the last of the four brains. BakingTray's Auto-ROI algorithm images only regions containing tissue and skips the empty space between brains.

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Rob Campbell @raacampbell.com · 04/10/2026

BrainSaw images whole brains. We acquire most of our data from 4 µm/pixel for (e.g. for brain-wide projection mapping), down to 1.2 µm/pixel to visualise single axons.

Bulk axonal projections spreading brain-wide from two injections (magenta and cyan). The mouse brain was imaged at 4 × 4 × 20 µm/voxel and downsampled to 25 µm isotropic. The volume is shown resliced in coronal, sagittal and horizontal planes. Scale bars 1 mm. Image credit: Chaofei Bao

Sst-tdTomato mouse brain; tdTomato in yellow, autofluorescence in blue. Top: coronal, horizontal and sagittal reslices through the whole brain, downsampled to 10 µm isotropic. Bottom: full-resolution detail (1.2 × 1.2 µm/pixel) showing bundles of individual axons in the cerebellum.

100 µm thick maximum intensity projection showing Purkinje cells in the rat flocculus. Imaged on BrainSaw at SWC. Image credit: Viktor Plattner.

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Rob Campbell @raacampbell.com · 04/10/2026

Preprint is out! Our BakingTray software turns a 2-photon microscope into a serial-section tomography system for automated whole-organ imaging. ~€35k to convert an existing scope. 11 systems worldwide, >7,000 samples at SWC alone #neuroskyence #microscopy www.biorxiv.org/content/10.6...

A BrainSaw at the Max Planck Institute for Brain Research, Frankfurt. A Nikon 16x water-immersion objective on a 400 µm travel PIFOC allows for fast z-stacks. Samples are imaged and cut in the clear water bath. A Leica VT1000 vibratome is seen to the right with a mounted blade.

How BrainSaw works. Samples are embedded in an agarose block, which is glued to a slide and clamped into a water bath. The bath sits on a three-axis stage under a 2-photon microscope; the stage moves the sample for both tile scanning and slicing. The microscope images the exposed face of the block, the vibratome cuts off the imaged layer, and the cycle repeats until the samples have been fully imaged. Data are stitched automatically and are ready for downstream analysis. Logos below: BrainSaw (hardware), BakingTray (acquisition software), StitchIt (stitching).

Coronal section of an Sst-tdTomato mouse brain imaged on BrainSaw. tdTomato-expressing cells are shown in yellow, scattered through cortex and hippocampus; tissue autofluorescence is shown in blue.

Coronal section of a mouse brain with three neighbouring viral injections targeting layer 5 of V1, expressing mCherry (red), eGFP (green) and BFP (blue). The thick apical dendrites of the labelled neurons are clearly visible, as are their axons projecting to distant targets. Image credit: Alex Fritzl.

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Rob Campbell @raacampbell.com · 06/09/2026

Our BrainSaw serial-section 2-photon platform acquires whole-organ datasets automatically and requires minimal tissue processing. It has a growing international install base and has contributed to 35 publications. Learn more at: swcmicroscopy.com/brainsaw/ #microscopy #neuroscience

A BrainSaw serial section 2-photon system. This particular example was modified from an TissueCyte 1000 commercial system. Others have been built from scratch or were modified from in vivo multi-photon systems. Each BrainSaw is unique, but all run BakingTray serial section 2-photon acqusition software that plugs into ScanImage.

Somatostatin tdTomato transgenic mouse imaged on BrainSaw serial section 2-photon. Full res images acquired at around 1 micron/pixel. Top images derived from 10 micron/voxel isotropic 3D stack.

Detail from a BakingTray acquisition obtained from a BrainSaw serial section 2-photon microscope. Image shows three AAV injections leading to expression of fluorescent proteins (mCherry, GFP, and BFP) in layer 5 neurons of mouse primary visual cortex. Imaged at 780 nm.

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Rob Campbell @raacampbell.com · 15/02/2025

I see it in the UK.

Maps showing text saying "gulf of Mexico (gulf of America)"

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Rob Campbell @raacampbell.com · 25/12/2024

Huh?

Film poster for the Movie "Tár" (2022) describing it as a comedy.

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Rob Campbell @raacampbell.com · 25/12/2024

Not bad. Just a bit darker next time. 😬

Mark Rothko, untitled (black blue). Last sold for 2.9 million pounds.

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Rob Campbell @raacampbell.com · 30/11/2024

Just realised that, back in April, when we by chance stopped in Lockhart (TX) for a coffee, we were where Season 2 of The Leftovers was filmed. Miracles happen.

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Rob Campbell @raacampbell.com · 29/11/2024

🧪🔬A pretty old picture for #fluorescencefriday but it's my favourite so it gets another outing. It's the drosophila mushroom body taken with a 2-photon and colour-coded for depth.

Drosophila mushroom bodies. Neurons shaded in red and yellow according to depth.

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Rob Campbell @raacampbell.com · 23/11/2024

Currently doing more validation experiments on our random access #optogenetics system for #neuroscience: Zapit. User-friendly GUI and documentation. Full build hardware build instructions coming soon. Cross-platform control (remote or local) from any language via TCP/IP. Build assistance available!

"Zapit" optogenetics system over a model mouse. The system is pointing a laser beam at the head of the model mouse and drawing the outline of a brain on the surface.

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Rob Campbell @raacampbell.com · 23/11/2024

No way! My memory made up the graph, it seems, but I found the book.

Quote stating the therapy is equally effective regardless of theoretical framework.

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Rob Campbell @raacampbell.com · 22/11/2024

A basic image for #fluorescencefriday -- neurons expressing the Ca++ sensor, GCaMP, imaged with a 2-photon microscope. The cool thing is the microscope is built by neuroscience students on our PhD optics course. It is the last thing they build at the end of their two week optics journey.

Image of a 2-photon microscope, showing posts, scanners, lenses, mirrors, etc, on an air-table

Researcher placing sample (a brain slice) under a 2-photon microscope.

Neurons expressing GCaMP calcium indicator in a brain slice imaged with a 2-photon microscope

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Rob Campbell @raacampbell.com · 17/11/2024

We made a "rainbow" of scattered light using a sucrose solution and polarized light for our annual PhD optics course. Thanks to @3b1b.bsky.social for making such great videos explaining the effect: www.youtube.com/watch?v=QCX6...

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