ALLEN CELL EXPLORER
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Glossary of cell features

Glossary of cell "feature" plotting axis terms

Picture
This glossary will be updated in February 2023.
In the meantime, you can hover over a feature's name in either axis to read a popup definition.
The following terms are used in the interactive plot of the Cell Feature Explorer. The cells can be plotted and colored by any measured feature.
cell height
Cell height: the height of a cell, as measured by the number of pixels that separates the bottom most and top most pixel in the segmented image converted to units of µm.
cell height
DNA height: the height of a nucleus, as measured by the number of pixels that separates the bottom most and top most pixel in the segmented image converted to units of µm.
cell height
Cell volume: the volume of a cell, as measured by the sum of individual volumes of segmented voxels in the segmented cell image, in units of µm3.
cell height
DNA volume: the volume of a nucleus of a given cell, as measured by the sum of individual volumes of segmented voxels in the DNA segmentation image, in units of µm3.
cell height
Cell surface area: the surface area of a cell, as measured by the sum of individual surface area of segmented voxels, in units of µm2.
cell height
DNA surface area: the surface area of a nucleus of a given cell as measured by the sum of individual surface area of segmented voxels, in units of µm2.
cell height
Cellular structure volume: the volume of the fluorescently labeled structure of a given cell, as measured by sum of individual volumes of segmented voxels, in units of µm3.
cell height
Anaphase segmentation complete:  Whether the segmentation contains the entirety of the cell boundary (only determined for cells in anaphase).
cell height
Interphase or mitosis: Whether a particular cell is currently in interphase or mitosis.
cell height
Interphase & mitotic stages: Which of 5 stages of the cell cycle (determined by the shape of the DNA) a particular cell is currently in.
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  • About
      Institute
      1. News feed
      2. What we do
      3. Publications
      4. Allen Institute | allenInstitute.org
      5. Careers
      Site
      1. Home page
      2. Site updates
      3. Archived content
  • Allen Cell Collection
      Order cells & plasmids
      1. Cell Catalog
      2. Cell Catalog quickview
      3. Cell Shorts (documentaries on labs using our cells)
      4. Support forum
      Lab methods
      1. Instructional videos for success in the lab
      2. Standard operating procedures (written methods)
      3. Illustrated overviews
      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
      Online image analysis
      1. Cell Feature Explorer (plotting & 3D viewer)
      2. 3D cell viewer (pre2018)
      3. Deep cell zoom (216,016 cells)
      Online modeling viewers
      1. Visual Guide to Human Cells
      2. Simularium (4D visual analysis)
      3. Integrated Mitotic Stem Cell
      4. └ Z-stack viewer
      5. └ 3D viewer
      6. Allen Integrated Cell viewer
      7. Label-free examples viewer
      8. 3D probabilistic model viewer
      Desktop tools
      1. Allen Cell & Structure Segmenter
      2. AGAVE 3D pathtrace image viewer
      Data & code
      1. Download cell data (images, genomics, features)
      2. Code repositories & software
  • Analysis & Modeling
      Allen Integrated Cell models
      1. Overview
      2. Integrated Mitotic Stem Cell
      3. └ Z-stack viewer
      4. └ 3D viewer
      5. Label-free Determination
      6. └ 3D viewer
      7. 3D Probabilistic Modeling
      8. └ 3D viewer
      9. Visual Guide to Human Cells
      4D biology models
      1. Simularium (online 4D viewer)
      Methodologies
      1. Drug perturbation pilot study
      2. hiPS cells during mitosis
      3. Differentiation into cardiomyocytes
  • Publications
      Articles
      1. All journal publications
      2. Preprints (biorxiv, arxiv)
      Posters
      1. Select posters
  • Education
      Education resources
      1. All Resources
      2. Teaching materials
      Online tools popular with teachers
      1. Visual Guide to Human Cells
      2. Integrated Mitotic Stem Cell
      3. Cell Feature Explorer (interactive plotting & 3D viewer)
      4. 3D cell viewer (pre2018 data)
      5. hiPS cell structure overview
  • Support
      Questions
      1. FAQs
      2. Forum
      Tutorials for digital tools
      1. Digital tool tutorials with videos
      2. Visual Guide tutorial
      3. AGAVE user guide
      Lab methods
      1. Instructional videos for success in the lab
      2. Standard operating procedures (written methods)
      3. Illustrated overviews
  • 🔍
      SEARCHBAR