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Job Summary The Cai lab is seeking a Software Engineer. The successful candidate will help develop software platforms for performing single cell image segmentation and spatial gene expression analysis. The candidate will also help the Cai lab convert these algorithms into production ready tools for the scientific community.
The candidate's primary role will be to help the Cai group pioneer the next generation of deep learning algorithms for single cell image segmentation and spatial gene expression analysis. Key duties and responsibilities include (but are not limited to):
Code existing deep learning architectures and generate novel deep learning architectures for image segmentation and cell tracking through 3D images
Test and document the performance of different deep learning architectures
Construct a production ready image analysis pipeline with version control
Construct tutorials for cloud computing and write blog posts
Create interactive image analysis notebooks with Jupyter
Assist with crowd sourcing of data set annotation
Interface our deep learning based image segmentation pipeline with existing GUIs
Assist with GUI development
Assist with grant writing and paper writing
Assist research group members with using the created software packages
Collaborate with Principal Investigator to determine direction of research
Author or co-author results
Other duties as assigned
Bachelor's degree in Computer Science or Bioinformatics or a related field
At least three years of experience working as a software developer
Working knowledge of Python (particularly the numpy/scipy/pandas/scikit-image/scikit-learn data science stack), Java, and C.
Working knowledge of calculus and linear algebra
Familiarity with modern deep learning methods and libraries (keras/tensorflow and/or Pytorch)
Working knowledge of modern version control packages (I.e git/github)
Excellent oral and verbal communication skills
Enthusiastic about the opportunity to engage with life science researchers
Master's degree in Computer Science, Bioinformatics or a related field
Extensive deep learning experience using either Keras/tensorflow and/or Pytorch
Experience in computational image analysis
Experience in cloud computing - both Google cloud engine and Amazon web service
Experience in creating interactive notebooks with Jupyter
Experience writing online tutorials and blog posts
We are an equal opportunity employer and all qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability status, protected veteran status, or any other characteristic protected by law.
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