What are you specifically working on?

More Susan Rehorek's questions See All

What are the sources of Embryo-Fetal vertebrate specimens?

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Where can I find an appropriate journal?

My colleague, Carolyn Steglich, and I are in the process of writing up some supervised undergraduate student research regarding the molecular analysis of the secretions of the garter snake...

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Where can I find atmospheric measurement profiles (temperature, density, etc.) between 300-800 km altitude?

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Which group formation theory do you recommend for projects that aim to bring together entrepreneurs for training for regional development?

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28 February 2021 4,223 2 View

What software programs can directly simulate Additive Manufacturing Directed Energy Deposition (DED)?

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I am looking for a simple software program to model 3D chemical bonds. The purpose is to generate high-quality graphical abstracts. Any suggestion?

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Which programs are to be used to register 2D image onto a 3D image data set?

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What is the better software for approximation of 3D surface with equations?

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How can I obtain Reaction Forces in ABAQUS?

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How to convert 2D stack images to 3D to obtain surface area of nucleus?

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How to get the vector of a specific vibration mode in phonon dispersion?

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Has anyone used deep learning for 2D/3D REGISTRATION ?

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Simone Gaffling

Thank you for your interest in our research! I will answer from a computer scientists point of view, and our anatomy expert will weigh in later on.

Our aim is to generate high-quality 3-D reconstructions based on serial sections, of all kinds of tissues/structures and stainings. We have already done several reconstructions, which include mouse brain and eye, pig lacrimal gland, and human embryos of different gestational age.

The main goal for high-quality reconstructions is the reversal of artifacts (like inhomogeneous staining and tissue deformations) while keeping the necessary image operations as minimal and realistic as possible.

To do so, we use custom software which is under active development.

What exactly are you interested in? Would you be interested in a reconstruction of one or several of your specimens?

Susan Rehorek

What program do you use? I am learning Amira (and it is fussy). Do you have specimens over there? Where are you physically located to do this? My interest lies in orbital and nasal reconstructions. I have a diverse series of specimens across vertebrata (I have the histology bit done).

We are located in Erlangen, Germany.

I've never myself worked with Amira, but I've see others using it, and it seemed very complex to use. The software we use was developed and implemented by a colleague of mine and myself. We are currently working on it to make it into a commercial software, and to be able to offer reconstructions as a service (we hope to be able to do this mid-2017).

If you are interested in seeing what we can achieve, I can offer you to do a reconstruction of a specimen of your choice, say up to ~100 slices. I could generate a dropbox directory for you to put the digitized images in, and we will see what we can do? No strings attached of course.

I've attached a detail of a reconstruction of a human embryo, and the reconstructions shown in the publications attached to this project are also done using our software.