Do you like deep learning, image processing, bioimaging and sunshine? 👩‍💻🔬📊🌞

We have a fantastic project available for a prospective PhD student at CCMAR Algarve! You can enroll on a PhD programme of your choice anywhere in Portugal (or event abroad, but special conditions apply). 👩🏻‍🎓

The EU-funded IMAGINE project (https://www.embl.org/about/info/imagine/) focuses on developing and integrating major disruptive imaging technologies to enable scale-crossing structural and functional investigation of biological specimens in their natural context. AI-powered image analysis capabilities will support technology integration and make data widely available. To harness the power of imaging for some of the most pressing societal challenges, IMAGINE will prepare its new imaging technologies to be deployed in the field, on Europe’s seas and coastlines, with the aim of coupling the collection of environmental specimens with their study using the highest resolution imaging. 

This research project focuses on the development of deep learning-based image reconstruction, processing and analysis software tools for different imaging modalities, mainly for lightsheet microscopy and optical projection tomography, but also for X-ray computed tomography (CT), magnetic resonance imaging (MRI) and other imaging techniques developed within the IMAGINE project. The candidate will develop an interactive user-friendly software tool based on supervised and self-supervised (model-based) deep learning methods for image reconstruction, segmentation, classification, etc, publish research papers together with open-source code that allows others to reproduce the results and present findings at international conferences.

The supervisory team consists of Dr. Teresa Correia (CCMAR Algarve) and Dr. Anna Kreshuk (EMBL). The successful candidate will join Dr. Teresa Correia’s Quantitative Bio-Imaging group at CCMAR (https://qbioimaging.github.io/). There will be opportunities for secondments with Dr. Anna Kreshuk (https://www.embl.org/groups/kreshuk/) at EMBL Imaging and Machine learning for Bioimage Analysis groups (Germany). 

The ideal candidate is expected to have:

• An MSc in Biomedical Engineering, ML/AI/DL, Computer Science, Physics, Optics, although degrees in other related physical sciences or engineering disciplines may be considered. 🎓
• Experience with bio-imaging data and be familiar with classical image processing and analysis algorithms 🔬🧲📉
• Proven Python programming skills and experience with common libraries such as scikit-image and scikit-learn 👨🏻‍💻
• Prior experience with machine learning and deep learning using Tensorflow or PyTorch 🤖🧠

Specifically, the fellowship holder will be involved in the following tasks:

• Development and/or implement deep learning-based image reconstruction, processing and analysis software tools 🛠️ for different imaging modalities, mainly for lightsheet microscopy and optical projection tomography, but also for computed axial  tomography (CT), magnetic resonance imaging (MRI) and other imaging techniques developed within the IMAGINE project. 
• Deploy methods as a plugin for Napari and/or ImageJ. 👨🏻‍💻
• Publish research papers together with open-source code that allows others to reproduce the results. 📑
• Present findings at international conferences. 👨‍🏫

📝 For more information and to apply go to: https://www.ccmar.ualg.pt/en/job/ccmarbincgam052023-research-fellowship-person-master-degree