Available Software
AGAVEα
α-testing prerelease code name for the Advanced GPU Accelerated Volume Explorer
α-testing prerelease code name for the Advanced GPU Accelerated Volume Explorer
Description: The volume viewer used path-trace rendering in an interface designed and optimized for the display of multi-channel, single-time OME TIFF files.
Requirements: This α release requires a computer running the latest version of Windows 10 and an NVIDIA graphics card with CUDA vX or newer. Future versions may run on less specific systems.
Instructions: Unzip the contents into a new directory on your Windows computer and open README.txt for detailed instructions to load and visualize volumetric data files.
Available code
The Allen Cell Structure Segmenter: a Python-based open source toolkit developed at the Allen Institute for Cell Science for 3D segmentation of intracellular structures in fluorescence microscope images.
Label-free Determination: Label-free prediction of three-dimensional fluorescence images from transmitted light microscopy
Integrated Cell: Image-driven generative cell modeling with adversarial autoencoders
Cell Shape Analysis Jupyter Notebook: What shape are our human induced pluripotent stem cells? Use a Jupyter notebook to help build intuition about shape across the population of cells available in the Allen Cell Collection.
Programmatic Data Access Jupyter Notebook: Learn how to downloading and accessing Allen Institute data using Quilt via a Jupyter Notebook.
More coming soon...
Our goal is to make all tools and software developed at the Institute publicly available once they are useful and robust. In the coming year, we will begin to post the code for various projects into open-source repositories.
With a goal of practicing and promoting open science, we use and develop open-source software whenever possible and practical. Licensing will be described as the software is released.
With a goal of practicing and promoting open science, we use and develop open-source software whenever possible and practical. Licensing will be described as the software is released.