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biology articles code imaging

Improving Z-resolution of lightsheet data using CARE upsampling

After posting the first version of our cephalic furrow pre-print, I received an email asking for further technical details about using the CARE upsampling module to restore the Z-resolution of lightsheet datasets: I am curious about some details of your “Pre-patterned epithelial invagination prevents mechanical instability during fly gastrulation” paper. You mention that you trained […]

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biology articles imaging

Denoising an old photomicrograph

Note: The denoising I describe in this post was done for artistic reasons and not for scientific purposes. For the proper methodology on image denoising, please follow the CARE paper. I wanted to denoise a twenty-year-old photomicrograph. It’s one of the first scientific images I created back in 2003. It’s so ancient that I used […]

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imaging articles code

ImageJ macro to synchronize and combine image stacks

When I film embryos under the microscope, some will be younger and some will be older than others—they are never in perfect synchrony. This is fine when watching the recordings of individual embryos, but becomes an issue when you want to watch two (or more) embryos developing side-by-side. In my case, I want to identify […]

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imaging biology notes

The surface of a brachiopod embryo

This is a brachiopod embryo at the gastrula stage, showing its outer surface and the blastopore at the bottom. To visualize the cell membranes, I stained the sample for F-actin (filamentous protein fibers present in cells) and acquired a volumetric image stack in a confocal microscope. Then, I converted the original data to a 3D […]