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Image analysis & visualization
▉ visualization
AGAVE
Powerful volume viewer with path-trace rendering to display multi-channel TIFF and OME-Zarr images |
▉ analysis ▉ visualization
Allen Cell & Structure Segmenter
napari plugin & open-source Python-based toolkit for 3D image segmentation |
▉ analysis ▉ visualization
Timelapse Feature Explorer (TFE)
Online tool to interactively visualize & analyze segmented time-series microscopy data |
▉ visualization
Vol-E
Online volume viewer to visualize your own volumetric data including OME-Zarr format |
▉ visualization ▉ education
Cell Feature Explorer
(CFE) Online tool composed of a scatterplot & 3D viewer to visualize segmented and processed hiPSC images from our open datasets |
▉ visualization ▉ education
Simularium
Online analysis tool to visualize, share and interrogate biological simulations |
▉ visualization ▉ education
Integrated Mitotic Stem Cell (IMSC)
Online educational tool that uses real-world data to provide a holistic view of human cell division |
▉ visualization ▉ education
Visual Guide to
Human Cell Online educational tool to interact with 3D cell models and learn about individual cell structures and functions |
Data support
▉python ▉ data support
BioIO
Image reading, metadata conversion, and image writing for microscopy images in pure Python |
▉ data management
BioFile Finder (BFF)
Online tool to curate, interrogate, and share datasets through rich metadata exploration & image viewing |
▉ data download
Data Download
Open-access datasets for download |
Code
▉ machine learning
CytoDL
Framework to unify and simplify deep learning approaches for analyzing biological data |
▉python ▉ analysis
Cell Variance Analysis
Processing of FOVs and cells for the Cell Variance Analysis |
▉ analysis
Other Codebases
Open-access code developed at the institute |
Cell lines
▉cell lines
Allen Cell Catalog
Quality control database of gene-edited hiPS cell lines |
▉cell lines
Disease Cell Collection
Quality control database of gene-edited cell lines that carry mutations in genes known to cause disease |
▉cell lines
Lab Plasmids
Deposited plasmids at Addgene for distribution to the research community |
▉cell lines
Standard operating procedures (SOPs)
Cell culture, differentiation, and microscopy protocols for gene-edited hiPSCs |
▉cell lines
Genomics
Open-access genomics and transcriptomics data of parental and gene-edited hiPS cell lines |