ALLEN CELL EXPLORER
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  • Allen Cell Collection
      Order cells & plasmids
      1. Cell Catalog
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      3. Cell Catalog quickview
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      About our hiPS cells
      1. hiPS Cell Structure Overview
      2. Visual Guide to Human Cells
      3. Cell structure observations
      4. Why endogenous tagging?
      5. Differentiation into cardiomyocytes
      6. Genomics
      7. Download cell data: Images, genomics, & features
  • Data & Digital Tools
      General
      1. Tools and resources overview
      2. Download cell data (images, genomics, features)
      3. Code repositories & software
      Desktop tools
      1. Allen Cell & Structure Segmenter
      2. AGAVE 3D pathtrace image viewer
      Web tools
      1. BioFile Finder
      2. Cell Feature Explorer
      3. Integrated Mitotic Stem Cell
      4. └ Z-stack viewer
      5. └ 3D viewer
      Web tools (con't)
      1. Simularium viewer
      2. Timelapse Feature Explorer
      3. Visual Guide to Human Cells
      4. Vol-E (Web Volume Viewer)
      5. 3D Cell Viewer
  • Analysis & Modeling
      Allen Integrated Cell models
      1. Visual Guide to Human Cells
      2. Integrated Mitotic Stem Cell
      3. └ Z-stack viewer
      4. └ 3D viewer
      5. Allen Integrated Cell
      6. └ 3D Probabilistic Modeling
      7. └ Label-free Determination
      4D biology models
      1. Simularium viewer
      Methodologies
      1. Drug perturbation pilot study
      2. hiPS cells during mitosis
      3. Differentiation into cardiomyocytes
  • Publications
      Articles
      1. Publications
      2. Preprints
      Presentations
      1. Talks & posters
  • Education
      Educational resources
      1. All resources
      2. Teaching materials
      Online tools popular with teachers
      1. Visual Guide to Human Cells
      2. Integrated Mitotic Stem Cell
      3. 3D Cell Feature Explorer
      4. 3D Cell Viewer
      5. hiPS cell structure overview
  • Support
      Questions
      1. FAQs
      2. Forum
      Tutorials for digital tools
      1. Video tutorials
      2. Visual Guide tutorial
      3. AGAVE documentation
      Lab methods
      1. Video protocols
      2. Written protocols
      3. Our methodology
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Code repositories & software

Available software

AGAVE
Advanced GPU Accelerated Volume Explorer
Picture
The volume viewer uses path-trace rendering in an interface designed and optimized for the display of multi-channel OME TIFF files. Learn more.
​Allen Cell & Structure Segmenter
Picture
The Python-based open source toolkit enables 3D segmentation of intracellular structures in fluorescence microscope images. Also available as a plugin for Napari. Learn more.

Available code

BioIO (replacing AICSImageIO): a Python library for reading & writing microscopy images of various formats. BioIO also provides services to unify and convert image metadata.  Find detailed documentation here.
CytoDL: aims to unify and simplify deep learning projects while making them modular and reproducible in order to advance understanding of 2D and 3D biological data as images, point clouds, or tabular data.
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.
Analysis 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.
Label-free Determination: Label-free prediction of three-dimensional fluorescence images from transmitted light microscopy
  • Label-free training data download
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.
Integrated Cell: Image-driven generative cell modeling with adversarial autoencoders

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.

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Allen Institute for Cell Science is a part of the Allen Institute. The mission of the Allen Institute is to understand the principles that govern life, and to advance health. Our creative and multi-dimensional teams focus on answering some of the biggest questions in bioscience. We accelerate foundational research, catalyze bold ideas, develop tools and models, and openly share our science to make a broad, transformational impact on the world.
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​Copyright © 2025 Allen Institute. All Rights Reserved.
  • About
      Institute
      1. Our science: CellScapes
      2. Past foundational projects
      3. News feed
      4. About us
      5. Careers
  • Allen Cell Collection
      Order cells & plasmids
      1. Cell Catalog
      2. Disease Collection Cell Catalog
      3. Cell Catalog quickview
      4. Cell video shorts
      Lab methods
      1. Video protocols
      2. Written protocols
      3. Our methodology
      4. Support forum
      About our hiPS cells
      1. hiPS Cell Structure Overview
      2. Visual Guide to Human Cells
      3. Cell structure observations
      4. Why endogenous tagging?
      5. Differentiation into cardiomyocytes
      6. Genomics
      7. Download cell data: Images, genomics, & features
  • Data & Digital Tools
      General
      1. Tools and resources overview
      2. Download cell data (images, genomics, features)
      3. Code repositories & software
      Desktop tools
      1. Allen Cell & Structure Segmenter
      2. AGAVE 3D pathtrace image viewer
      Web tools
      1. BioFile Finder
      2. Cell Feature Explorer
      3. Integrated Mitotic Stem Cell
      4. └ Z-stack viewer
      5. └ 3D viewer
      Web tools (con't)
      1. Simularium viewer
      2. Timelapse Feature Explorer
      3. Visual Guide to Human Cells
      4. Vol-E (Web Volume Viewer)
      5. 3D Cell Viewer
  • Analysis & Modeling
      Allen Integrated Cell models
      1. Visual Guide to Human Cells
      2. Integrated Mitotic Stem Cell
      3. └ Z-stack viewer
      4. └ 3D viewer
      5. Allen Integrated Cell
      6. └ 3D Probabilistic Modeling
      7. └ Label-free Determination
      4D biology models
      1. Simularium viewer
      Methodologies
      1. Drug perturbation pilot study
      2. hiPS cells during mitosis
      3. Differentiation into cardiomyocytes
  • Publications
      Articles
      1. Publications
      2. Preprints
      Presentations
      1. Talks & posters
  • Education
      Educational resources
      1. All resources
      2. Teaching materials
      Online tools popular with teachers
      1. Visual Guide to Human Cells
      2. Integrated Mitotic Stem Cell
      3. 3D Cell Feature Explorer
      4. 3D Cell Viewer
      5. hiPS cell structure overview
  • Support
      Questions
      1. FAQs
      2. Forum
      Tutorials for digital tools
      1. Video tutorials
      2. Visual Guide tutorial
      3. AGAVE documentation
      Lab methods
      1. Video protocols
      2. Written protocols
      3. Our methodology
  • 🔍
      SEARCHBAR