Available SoftwareAGAVE
Advanced GPU Accelerated Volume Explorer 
Description: The volume viewer uses path-trace rendering in an interface designed and optimized for the display of multi-channel OME TIFF files.
Requirements: This stable release requires a computer running the latest version of Windows 10 or Mac OS 10.12 or newer.
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.
Windows only: The first time you run AGAVE, if you see an error message about missing VCRUNTIME140_1.dll, then you need to download and install vc_redist.x64.exe from this link. After the install, AGAVE should start normally. |
Available codeAnalysis code for the manuscript Cell states beyond transcriptomics: integrating structural organization & gene expression in hiPSC-derived cardiomyocytes. GitHub notebook for figures produced for the study. AICSImageIO: a Python library for reading & writing microscopy images of various formats. AICSImageIO also provides services to unify and convert image metadata. Find detailed documentation here. 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. Programmatic Data Access Jupyter Notebook: Learn how to download and access Allen Institute data using Quilt via a Jupyter Notebook. 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. |
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.