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Python Developer

1 month ago

Madison, United States Sundial Software Full time

seeking a skilled Python programmer to work with our Amira/Aviso 3D electron microscope imaging package. Our goal is to extend this package with a plugin that utilizes hyperspectral imaging data from our optical microscopes. This project involves leveraging the machine learning training infrastructure and imaging segmentation within the Amira/Aviso package to develop models for targeted imaging or post collection results on our optical microscopes. We plan to use this project internally as the basis for an early adopter, assuming that the TRL5 early adopter will be in-house. Key requirements for this role include:

  • Proficiency in Python programming.

  • The ability to learn and work with the Amira/Aviso 3D imaging package (Amira-Avizo Software | Getting started (youtube.com)).

  • Access to our network through a Thermofisher PC/VPN, as the Amira/Aviso package is licensed through our systems. Originally, we had slated this project at approximately 0.25 YEFE (Yearly Effective Full-Time Equivalent). While on-premise work is beneficial for demonstrations, remote work is also feasible.

There will be a learning curve, and we will provide the necessary training materials to ensure the programmer can efficiently use the package to the extent to develop the required plugin. We are looking for someone who can quickly get up to speed and drive this project forward.

Preliminary execution plan (still need to finalize for SOW):

Design Phase:

  • Select appropriate languages and frameworks for the application

  • Develop a high-level architecture diagram for the application

  • Define the data flow for the training pipeline

Development Phase:

  • Development Environment Setup

  • Implement the initial version of the hyperspectral model training plugin for Avizo/Amira. The data should be a 2D optical image and the associated 3D spectral data of the entire or sections of the 2D optical image. the 3D spectral data is provided for helping to label the image for targeting or for result processing as features for the model. We will work toward and acceptable data set to use in training.

  • Tests for individual functions and modules

  • Use simulation to simulate individual components and interfaces.

  • Ensure a clean and intuitive UI design

  • Design the user interface (UI) separately from the functionality

  • Identify training material and path that would facilitate usage of the plugin

Review and Adjustments:

  • Demonstrate individual functions, modules, example pipelines and model training

  • Regular review meetings to track progress and address issues

  • Ensure all requirements and goals are met before project completion