Available Software

AGAVEα
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 or newer. We will post a Mac build before May 25, 2019.

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.

Download AGAVE for Mac OS

Download AGAVE for windows

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

• Label-free training data download

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 download and access 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.