Highlights

Allen Cell Structure Segmenter

​We present the Allen Cell Structure Segmenter, a python-based, open-source toolkit that combines classic 3D image segmentation with artificial intelligence to detect cellular structures.

​Read more about this new toolkit and how it can help biologists analyze their 3D images of cells and be more quantitative with their results.

A visual essay on the Integrated Mitotic Stem Cell

​We present the Integrated Mitotic Stem Cell as a data driven model and visualization tool that captures a holistic view of human cell division for the first time.

​By enabling a deeper understanding of how healthy human cells divide, the model will further basic biology research as well as studies of cancer, a disease that often results from cell division gone awry.

New resources to access mitotic stem cell states & endogenously tagged cardiomyocytes

Cell Feature Explorer

Plot & view any of 39,200 3D cell images sorted by their features

Cell Catalog

4 new fluorescently-tagged hiPSC lines available in the Allen Cell Collection

Integrated Mitotic Stem Cell

A model & visualization tool to better understand how stem cells divide
The new lines include single tags targeting a muscle-specific actin filament, a pluripotent transcription factor, and a dual tag targeting nucleolar substructures. In addition, we released an additional cytoplasmic-expressing control line.

Previous highlights

Visual Guide to Human Cells
This visual guide organizes information about human induced pluripotent stem cells into a curated collection of interactive models. Users can rotate and zoom into 3D cells, each segmented from real data for each phase of mitosis, while learning more about individual cell structures and functions.
Label-free Determination
As part of the Allen Integrated Cell, we have developed and implemented a label-free prediction method for determining the location of 3D structures inside the cell, directly from transmitted light images.

Videos & tutorials

Instructional videos provided to ensure success in your lab & to overview tools available on allencell.org

Cells & plasmids for your lab

​We have created a series of gene edited human iPSCs that we use as the foundation for our image data, and that we share with the larger scientific community.
Obtain cell lines & plasmids for your lab​; quality control details
​Explore & download genomics & transcriptomics data
Step-by-step protocols to generate & image gene-edited hiPSCs successfully

Research Projects described

Observations describing effects of drugs on 3D cellular organization
Multiple cell structures visualized direct from brightfield imaging
3D visualization of hIPS cell structure variation
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