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Supplementary materials for the following publication in Nature:
Integrated intracellular organization and
​its variations in human iPS cells
Back to article

Supplementary Video 3

Overview panel of average morphed cells for 25 cellular structures reconstructed throughout the cell and nuclear shape space.
Each row represents one of the 25 cellular structures, indicated by the color bar on the far left. Each column represents Shape Modes 1-8, respectively. Each frame of the video represents one of the nine map points bins (Fig. 2b; in σ units, indicated at top left) along each shape mode and shows the resultant average morphed cells for the cells in that bin (numbers of cells in Supplementary Data 1​. For every cell the top view and side view 1 are shown. Heatmaps as in Extended Data Fig. 5.
​Scale bars are 5 μm.

Supplementary Video 4

Overview panel video of 25 cellular structures in edge and shape-matched non-edge cells​.
a. Within each half, either moving left to right (non-edge cells) or right to left (edge cells), two sets of two individual cell examples of the structure segmentation, the result of morphing that cell’s PILR into the combined non-edge + edge mean cell shape, and the resultant average morphed cells, visualized as in Extended Data Fig. 5.
b. PILR-LDA based reconstructions of average morphed cells at five positions (in σ units; each position is a frame inthe video, indicated by the arrowhead) along the non-edge to edge cell LDA axis. Histograms show frequency of cells along the LDA axis within non-edge (black) and edge (red) cell populations. Dotted vertical lines indicate the means. X indicates that LDA axis primarily identified technical differences in the PILR (Supplemental Methods). Heatmaps as in Extended Data Fig. 5.
Scale bars are 5 μm.

Supplementary Video 5

Overview panel video of 25 cellular structures in early mitosis.
a. Sets of two columns showing example(s) of individual cell structure segmentations and the resulting average morphed cells for all four early mitotic populations (i1, i2, m1, m2) in the appropriate mean mitotic cell shapes, visualized as in Extended Data Fig. 5.
b. PILR-LDA based reconstructions of average morphed cells at five positions (in σ units; each position is a frame inthe video, indicated by the arrowhead) along the i1 to m1 (left) and i2 to m2 (right) LDA axes. Histograms show the frequency of i1 and m1 cells or i2 and m2 cells along the LDA axis. Dotted vertical lines indicate the means. X indicates that LDA axis primarily identified technical differences in the PILR (Supplemental Methods). Heatmaps as in Extended Data Fig. 5. 
Scale bars are 5 μm.

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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