October 5, 2017 update

Five new cell lines are now available from Coriell. To help you explore these new cell lines, we have released the first in a series of tutorial videos that will either overview or teach how to use features and tools available on allencell.org.
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Other updates to allencell.org include:

Home
  • News. A link to a Gene Editing webinar and an article announcing new cell lines added to the News.
    • Webinar: Using CRISPR/Cas9 to Model Stem Cell Organization & Dynamics
    • Five new cell lines added to the Cell Catalog
  • Help is now Tutorials. We have changed the title of Home/Help to Home/Tutorials and present our first video tutorial on that page.
    • We renamed “Help” to “Tutorials”. The page is now located in the same menu group (under Home) at http://www.allencell.org/tutorials.html.
    • Amanda Haupt represents the Gene Editing group to present an overview of the Cell Catalog tool available on allencell.org available as a video on the Tutorials page.

Research Updates
  • Cell Stories / Get to Know the Cells. A new research update story has been added describing the behavior of cardiomyocyte differentiated cells: After differentiation of the edited stem cells into cardiomyocytes, cells begin to beat spontaneously.
  • Cell Stories / Cell Observations. Observations recorded on the five cells lines listed below, which were added to the Cell Catalog in September, have been added to the Cell Observations page:
    • New videos and observations:
      • LAMP-1 targeting lysosomes
      • Sialyltransferase 1 targeting Golgi (monoallelic)
      • Sialyltransferase 1 targeting Golgi (biallelic)
    • Updates to previous videos and observations:
      • α tubulin targeting microtubules (with mTagRFP-T); updated from 3/20/17
      • Centrin-2 targeting centrosomes; updated from 3/20/17

Cells
  • Cell Catalog. Five cell lines described in the Cell Catalog in September are now available in the Allen Cell Collection from Coriell. The Cell Catalog page has undergone a minor redesign to include:
    • “New” tags are displayed in green at the end of the Cell Line Protein Name on the first page of the Cell Catalog table to highlight the most recently released cell lines.
    • A “Cell Catalog Update” section highlights news related to the Cell Catalog and the Allen Cell Collection.
    • A short video tutorial overviews features of the Cell Catalog.

Methods
  • Detailed Methods / SOPs. Four new SOPs have been added to the Detailed Methods / SOP page.
    • A new SOP for Manual staining of WTC cells with CellMask Deep Red and NucBlue Live (for live-cell visualization of the plasma membrane and DNA) has been added to the Detailed Methods page.
    • A new SOP for Microscopy Pipeline Workflow - Image Acquisition (summarizing the steps required to acquire experimental and control images for the Microscopy pipeline data generation for the Integrated Cell project) has been added to the Detailed Methods page.
    • ​A new SOP for Sub-resolution and focal check beads solution for alignment and PSF measurements (summarizing steps to prepare the mixed-beads control in well G9 of a pipeline 96-well plate) has been added to the Detailed Methods page.
    • A new SOP for Fluorescent dye stock solutions for Flat Field Correction (describing how to prepare stocks of fluorescent dye solutions from solid powder and the further dilution required to make the working Flat Field solutions) has been added to the Detailed Methods page.

September 1, 2017 update

​Five new cell lines have been completed and will soon be available from Coriell. Details of which lines and the extensive quality control information for each line are available in the Cell Catalog pages. Z-stack movies displaying examples of volumetric images collected from these Cell Lines have been added to the Cell Image Gallery page.

​Other updates to allencell.org include:
​
Home
  • News. An announcement for a presentation from our Gene Editing team has been added to the News.
    • Webinar: Using CRISPR/Cas9 to Model Stem Cell Organization & Dynamics

Research Updates
  • Publications. One new article has been added to the list of scientific publications from Allen Institute for Cell Science researchers.
    • Systematic gene tagging using CRISPR/Cas9 in human stem cells to illuminate cell organization
      We present a CRISPR/Cas9 genome editing strategy to systematically tag endogenous proteins with fluorescent tags in human induced pluripotent stem cells.
    • The BioRxiv pre-print version of this paper temporarily links to the MBoC preprint version until the BioRxiv final becomes available.

Cells
  • Cell Catalog. Five cells lines, addressing four new targets have been added to the Cell Catalog. One of these new lines includes both a mono and bi allelic version, which prompted us to reformat the Cell Catalog page. The new Cell Catalog has a a simpler column layout, with fewer columns overall and two new columns that incorporate descriptors for the tagged allele (mono vs bi) and a thumbnail image.
    • LAMP-1 targeting lysosomes
    • Sialyltransferase 1 targeting Golgi (monoallelic)
    • Sialyltransferase 1 targeting Golgi (biallelic)
    • α tubulin targeting microtubules (with mTagRFP-T)
    • Centrin-2 targeting centrosomes
  • Cell Image Gallery. Z-stack movies displaying examples of volumetric images collected from the 5 new cell lines listed above have been added to the Cell Image Gallery.

July 1, 2017 update

A voxel size scalar used to calculate the Cell Feature Analysis Data has been corrected and the data updated to version 1.7. This revises the data on three pages of the website (two applications of the interactive plotting tool and on the Feature Analysis Data Download page) as detailed below.

​Other updates to allencell.org include:

Research Updates
  • Publications. Two posters presented at the recent ISSCR conference in Boston have been added under an Abstracts & Posters heading.
    • Creating an open source collection of GFP-tagged human iPSC lines to model stem cell organization and dynamics
    • Creating a Cardiomyocyte Pipeline for Gene Edited Human iPSCs

Tools & Data
  • 3D Cell Viewer. This page has undergone changes to the cell Feature data:
    • Values for size related cell features used on the axes for the Tools/Analysis panel of the 3D Cell Viewer, that come from Feature Analysis Data, have been updated to version 1.7. This only affects axis values, the relative positions in the scatter plots remain unaffected.
    • You may need to clear your cache or force a refresh of your browser window to access the new version, e.g. if using Chrome, hold the control key (Windows) or the shift key (Mac) and click the refresh button.
  • Interactive Plotting. Data update
    • Values for size related cell features that come from Feature Analysis Data have been updated to version 1.7. This only affects axis values, the relative positions in the scatter plots remain unaffected.
  • Feature Analysis Data Download. Data update
    • New file, version 1.7 with updated values for size-related features posted as aics_cell-feature-analysis_v1.7.csv.zip.

Methods 
  • Detailed Methods / SOPs. One SOP has been added.
    • A new SOP for scale up and banking of cell lines has been added to the Detailed Methods page.

June 1, 2017 update

The 3D Cell Viewer tool on the website has undergone a user interface overhaul and functionality additions. The June 1 update merges the interactive plotting tool functionality directly into 3D Cell Viewer's online browser interface. Users can now explore relationships across thousands of cells as graphical plots, visualize any of the data points as 2D projections of the cells, and load any of the data points (cells) into the volumetric viewer to explore the details of that cell in 3D. More details are provided in the Tools & Data section below.

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Other updates to allencell.org include:

Home
  • News. A presentation and two articles have been added to the News:
    • Photos from the Allen Cell Explorer presentation at NVIDIA’s GPU Technology Conference.
    • High Content Review and The Stem Cell Podcast ran feature stories on the Allen Cell Explorer.

Research Updates
  • Publications. Two new articles have been added to the list of scientific publications from Allen Institute for Cell Science researchers.
    • Generative Modeling with Conditional Autoencoders: Building an Integrated Cell
      This article details the deep learning approaches used to generate the integrated cells presented in the April 5, 2017 release of the Allen Cell Explorer. The code has also been provided as described in the Tools & Data / Software & Code update below.
    • Whole cell maps chart a course for 21st-century cell biology
      Plotting a course to understand human cell biology will require collaboration across disciplines, funding agencies, and research efforts, from individual investigators to large consortia.

Modeling
  • ​Integrated Cell Models. Links provided to the Generative Modeling with Conditional Autoencoders: Building an Integrated Cell paper described in Publications above to better describe the methods used.

Tools & Data
  • 3D Cell Viewer. This page has undergone several major changes:
    • User adjustable columns. Resize the Images, Viewer, and Tools columns independently
    • Faster filtering in the Images column
    • More intuitive user experience with improved tool layout and design
    • Cell image data now sorted by name to group cells from the same field together
    • Interactive plotting tool added directly to the interface to merge cell feature plotting with 3D viewing
    • Selecting a cell or field from any part of the user interface highlights that cell in the Images gallery
    • Bug fixes and improved layout of many user widgets
    • You may need to clear your cache or force a refresh of your browser window to access the new version, e.g. if using Chrome, hold the control key (Windows) or the shift key (Mac) and click the refresh button.
  • Interactive Plotting. Minor bug fixes.
  • Software & Code. The image-driven generative cell modeling with adversarial autoencoders code has been provided on GitHub.

Cells
  • Cell Catalog. Four new cell lines have been added to the Cell lines in progress section of the Cell Catalog: ​
    • ​PMP34 targeting peroxisomes
    • Rab-5A targeting endosomes
    • Safe harbor locus (AAVS1) targeting plasma membrane
    • Connexin-43 targeting gap junctions

Methods 
  • Detailed Methods / SOPs. One SOP has been updated and a new SOP added.
    • A new ddPCR screening SOP has been added on the Detailed Methods page.
    • The WTC SOP version 1.0, released April 5, 2017 has been updated to version 1.1
  • FAQs. A new question, "How do you visualize and present large 3D images in a web browser?" answered.