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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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biology imaging notes

The blastopore of bryozoan embryos

This is a bryozoan embryo with its blastopore facing us. The blastopore is the hole in the middle. The “balls” are the nuclei of the cells that make up the embryo. While cells have many other structures, they are not visible in this image. The only thing visible is the DNA because I stained it […]

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biology imaging notes

Chubby ribbon worm

A chubby ribbon worm juvenile #Nemertean #WormWednesday

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biology imaging notes

Larva of a lamp shell

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biology imaging notes

Fruit fly embryo under lightsheet microscopy

A short video that I made about the embryonic development of the likeable Drosophila, also known as fruit fly or vinegar fly, won an honorable mention in the Small World in Motion. The details on the techniques I used and the video on its full resolution are available for download and re-use on the Wikimedia […]

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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 […]

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imaging notes

A typical lightsheet microscopy session

Here is how a typical session of imaging embryos under Lightsheet Microscopy goes. A glimpse into my day-to-day work :) Assemble the incubation chamber: Collect and mount the embryos: Acquire a short timelapse from multiple angles: Transfer (lots of) data for image processing ;)

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biology imaging notes

The pelagosphera larva of Sipuncula

The pelagosphera larva of #Sipuncula. Photo by Alvaro Migotto via @cifonauta http://cifonauta.cebimar.usp.br/photo/10874/

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biology imaging notes

A beautiful nemertean

The ribbon worm Tubulanus #WormWednesday #Nemertea

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imaging biology notes

Eye imaginal disc of Drosophila

The eye imaginal disc of Drosophila (blue=elav, pink=repo, yellow=hrp) prepared with @Bugs_and_Slugs @ZVavrusova @zeiss_micro #embryo2017