May 27, 2021 update

Introducing the MegaMenu for improved navigation on allencell.org

Picture
AllenCell.org MegaMenu screenshot
We made major upgrades to your website navigation experience on allencell.org!
​The navigation menu has been reorganized and categorized,
​with many pages renamed (old URLs will automatically redirect).

April 21, 2021 update

New cells have been added to the database. Tools have been upgraded.

Detailed updates to allencell.org include:
Tools & Data
  • Cell Catalog. We have one new fluorescently tagged hiPSC line available in the Allen Cell Collection. The line is a single edited, nuclear line in which telomeres are visualized via mEGFP-tagged TRF2.
    The Allen Cell Collection (below) now has 48 high quality-certified fluorescently tagged hiPSC lines that target 38 key cellular structures and substructures available to help your research program.
  • Cell Feature Explorer. Code efficiencies reduce large dataset (216,000+ cells) download 10x to an average of 7 seconds.

December 21, 2020 update

Simularium Viewer released. Visualize, analyze, interrogate & share biological simulations directly in a web browser!

Detailed updates to allencell.org include:
Tools & Data
  • Simularium. Simularium makes it easy to share and analyze spatial simulations directly in a web browser. Its primary goal is to facilitate collaborations between experimental biologists and computational biologists by removing major challenges to accessing, running, sharing, and analyzing simulation results.
  • Cell Feature Explorer. This tool has many speed enhancements and plotting data efficiencies. It now supports multiple datasets including the newly released hiPSC Single-Cell Image Dataset v2020.1 (in review)
  • Software & Code. The Advanced GPU Accelerated Volume Explorer (AGAVE) has been upgraded from an α to a v1.0 release. The new version supports:
    • scene selection dialog when opening multiscene files
    • added support for loading files with 8-bit intensities
    • new documentation
    • updated Qt to 5.15 LTS
    • minor bug fixes with JSON save and load
    • improved logging

August 6, 2019 update

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.

Detailed updates to allencell.org include:
Tools & Data
  • Segmenter. A new webpage added to provide access to a new tool, the Allen Cell Structure Segmenter: A Machine learning toolkit that lets biologists navigate their way through a 3D cell.

May 22, 2019 update

The Allen Institute today released the Integrated Mitotic Stem Cell, a data-driven model and visualization tool that captures — for the first time — a holistic view of human cell division. 

Detailed updates to allencell.org include:
Modeling & Analysis
  • Integrated Mitotic Stem Cell. A new webpage added to provide access to a new model, the Integrated Mitotic Stem Cell, which is an scrollytelling webpage with two interactive 3D cell viewers, describing changes that occur in over a dozen cell structures during mitosis... other than DNA and microtubules!

January 11, 2019 update

New cells have been added to the database. Two new tools that are still in initial phases of development have been released.

Detailed updates to allencell.org include:

Home (now accessed via the Allen Cell Explorer logo)   
  • Highlights section updated with links to: 
  • Older highlights remain visible below the top highlight until they get moved into a highlights archive. The Highlights Archive will be available later this year.
​
Animated Cell
  • Research Projects. 
    • Educational Resources. This new page provides a list of pages on allencell.org that educators have used in their classrooms. It also has a new video presentation where three educators who use various features of allencell.org in their classrooms presented their curricula and data applications to an audience at ASCB in December 2018. entitled: 
      Cell Data in the Classroom: Using the Allen Cell Explorer in High School and College Education
      by Carlos C Goller, Tom Martinez, & Eric Shelden with Kaitlyn Casimo and Graham T. Johnson
    • More... This submenu has been removed.
      • Videos & Tutorials. Content from this page, formerly called Instructional Videos & Tutorials ​for Animate Cell Tools has been consolidated with the other categories of Videos & Tutorials into a single page now under About / Videos & Tutorials. ​​
      • Visual Guide Tutorial. This is a temporary page. The content is being moved to the consolidated page now under About / Videos & Tutorials. ​​
      • A new written tutorial: Visual Guide to Human Cells shows users how to use the Visual Guide to access an interactive overview of hiPS cell 3D structure & function. An introduction to the tutorial further explains why cells imaged with optical microscopy such as the Spinning Disc Confocal images we collect at the Allen Institute for Cell Science may look the way they do.
      • Methods. This page has been removed since the content is covered in other areas of the site. There had not yet been any Visualization specific Methods content posted on this page.
      • Software & Code. An alpha version of the Advanced GPU Accelerated Volume Explorer (AGAVE-α) has been posted. AGAVE is a volume viewer that uses path-trace rendering in an interface designed and optimized for the display of multi-channel, single-time OME TIFF files. The alpha release works on Windows 10 systems with NVIDIA/CUDA graphics only, but future versions may run on less specific systems.

Cells & Biology. Several placeholder pages previously found under this menu have been cleaned up as follows:
  • Research Projects.
    • hiPS Cells During Mitosis Last two figure legends describing tight junction behavior in mitosis corrected to describe ZO1 instead of mitochondria (website data entry error).
    • Segmenter.  This new page was miscategorized and quickly moved to Data & Tools / Research Projects / Segmenter. The content for this page is described below.
  • More... This submenu category has been renamed to become Methods & SOPs.
  • Methods & SOPs.
    • Methods. This page has been renamed to become Methods for Cells in the Lab.
    • Methods for Cells in the Lab. This page has been changed from the former name of Methods. A protocol has been updated.
      • list method updates
    • Videos & Tutorials. This page has been renamed to become Cell Methods: Videos from the Lab
    • Cell Methods: Videos from the Lab. 
      • list video updates
    • Software & Code. Content from this page, formerly called Laboratory software & code has been consolidated with the other categories of Software & Code into a single page now under Data & Tools / Software & Code. This page had not yet been populated with any software and code for use in the lab, but there are software and code links available for many other categories available on the consolidated page.

Microscopy.  This page is now called Tools & Data

Tools & Data. This top-level menu category has changed names from Microscopy to Tools & Data to clarify navigation on allencell.org.
Content from the four pages from this top-level menu category, which were the 3D Cell Viewer, Deep Cell Zoom, Research Projects, Data Downloading, and More.../Methods can still be found under this new name Tools & Data along with many new and reorganized pages.
  • Cell Catalog. We've added a second menu item to help users find the Cell Catalog more easily. A menu pointer to the exact same Cell Catalog web application also be found under Cells & Biology / Cell Catalog.
  • Cell Feature Explorer. This new tool prioritizes data analysis to help users find relationships or cells of interest more easily among the 10s of thousands of cells available in our online image collection. It contains the same data that the 3D Cell Viewer has available as well as a 3D Volumetric Viewer, but also contains data for new cells added since December 2018. Improvements will be made to this tool in the coming months and the 3D Cell Viewer will gradually be phased out with the Cell Feature Explorer replacing it.
  • Data Downloading. New cell image files available.
  • Data & Tools Research Projects.
    • Segmenter.  This new page describes a new tool we've made available while still in development called The Allen Cell Structure Segmenter, which is  a Python-based open source toolkit developed at the Allen Institute for Cell Science for 3D segmentation of intracellular structures in fluorescence microscope images. ​
  • Software & Code. Content from the various categorized Software & Code pages has been consolidated with the other categories of Software & Code this new single location.
    • An alpha version of the Advanced GPU Accelerated Volume Explorer (AGAVE-α) has been posted. AGAVE is a volume viewer that uses path-trace rendering in an interface designed and optimized for the display of multi-channel, single-time OME TIFF files. The alpha release works on Windows 10 systems with NVIDIA/CUDA graphics only, but future versions may run on less specific systems.
  • More...  This submenu has been removed.
    • Videos & Tutorials. Content from this page, formerly called Modeling Videos & Tutorial has been consolidated with the other categories of Videos & Tutorials into a single page now under About / Videos & Tutorials. The deprecated page had two videos that are accessible directly at https://www.allencell.org/videos--tutorials-collected.html#sectionAllenCellTutorials
    • Methods. Methods for microscopy has been renamed and moved to become /Cell & Biology / Methods & SOPs / Methods for Microscopy
    • Software & Code. Content from this page, formerly called Microscopy Software & Code has been consolidated with the other categories of Software & Code into a single page now under Data & Tools / Software & Code. This page had not yet been populated with any software and code for use in microscopy.

Modeling & Analysis. Several placeholder pages previously found under this menu have been cleaned up as follows:
  • ​More...  This submenu has been removed.
    • Videos & Tutorials. Content from this page, formerly called Modeling Videos & Tutorial has been consolidated with the other categories of Videos & Tutorials into a single page now under About / Videos & Tutorials. The deprecated page had not yet been populated with any Videos or Tutorials specific to modeling, but there are tutorials about many other subjects available on the consolidated page.
    • ​Methods. The Methods for Modeling & Analysis page has been removed because the community can access any methods used directly in the collected Software & Code github repository links or in the Publications.
    • Software & Code. Content from this page, formerly called Laboratory software & code has been consolidated with the other categories of Software & Code into a single page now under Data & Tools / Software & Code. This page had not yet been populated with any software and code for use in the lab, but there are software and code links available for many other categories available on the consolidated page.

News.  This top-level menu category is now called News & Publications

News & Publications. This top-level menu category has changed names from News to News & Publications to clarify navigation on allencell.org. The three of the four pages found under this top-level menu category, have not changed, and one submenu called Collected Content has been removed and its content moved to a new menu.
  • News Feed. Links to 2 new articles.
    • list news articles
  • ​​​Publications. One new article added.
    • list new publications
  • ​Collected Content. This landing page, which formerly contained only Videos & Tutorials Collected has been removed, and that subpage has been moved to a new location to ease navigation based on user feedback.

September 20, 2018 update

Our article Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy has been published in the September 2018 issue of Nature Methods.
A page on allencell.org describing the Label-Free Determination has been extended to include links to software and training data. Jove has released a new video detailing techniques we use for endogenous protein tagging.

Detailed updates to allencell.org include:

Home (now accessed via the Allen Cell Explorer logo)     ​
Cells & Biology Modeling & Analysis  The Modeling & Analysis category 5 new major content pages and 2 new landing pages.
  • ​Label-free determination graduated from a Research Project to become a full page. Use label-free determination to image with unprecedented clarity compared to other tagging methods.
  • Modeling & Analysis Research Projects. 
    • ​Label-free determination moved out from under /Research Project to become Modeling & Analysis / Label-free determination

News  ​

August 5, 2018 update

Five more fluorescently tagged hiPSC lines have been added to the Allen Cell Collection. The new lineup includes two new nuclear structures and three cardiomyocyte-specific structures.  Several pages were fine-tuned following the major updates to allencell.org in April and May.

Detailed updates to allencell.org include:

Home (now accessed via the Allen Cell Explorer logo)   
  • Highlights section focused on the Visual Guide to Human Cells.
  • Link to a release article describing the Visual Guide to Human Cells provided.
  • Older highlights remain visible below the top highlight until being moved into a highlights archive later this year.
 ​
Cells & Biology
  • More... 
    • Videos & Tutorials. A new video added
      • Allen Cell Methods: Setting up the WTC parental line for cardiac differentiation

News  ​

June 1, 2018 update

Two new videos released and several pages were fine-tuned following the major updates to allencell.org in April and May. Publications that were previously found under each major menu category are now found on a single Publications page.
​
Detailed updates to allencell.org include:

Animated Cell
  • More... 
    • Publications. This sub page was deleted and its content moved to https://www.allencell.org/publications.html.

Cells & Biology
  • More... 
    • Videos & Tutorials. 2 new videos added
      • Overview of our gene editing process
      • Allen Cell Methods: RNP transfection for gene-editing human iPS cells
    • Publications. This sub page was deleted and its content moved to https://www.allencell.org/publications.html.
 
Microscopy
  • Deep Cell Zoom. An interactive 2D zoomable display showing all of the cells available in the 3D Cell Viewer.
  • More...  
    • Publications. This sub page was deleted and its content moved to https://www.allencell.org/publications.html.

News  ​

April 25, 2018 update

The allencell.org website is undergoing a major update. Several new pages are being released throughout the day on April 25, 2018, and will be listed here as they occur.
​
Detailed updates to allencell.org include:

Home (now accessed via the Allen Cell Explorer logo)   The Home page has 6 new sections describing new or updated content you can find deeper in the site of allencell.org. Page descriptions on the Home page are often organized into different categories compared to the categories already provided by the top level menu.
  • Highlights section focuses on the Allen Integrated Cell.
  • Website allencell.org reorganized
  • New ways to explore our data
  • Cells for your lab
  • 4 new Research Projects described
  • Videos & tutorials

About
  • What we do. Text overviewing the mission and methods of the institute has been updated in the Overview of the Allen Institute for Cell Science workflow section.
​
Animated Cell  This new menu category summarizes what we are learning about cells at the Allen Institute for Cell Science with engaging tools.
Cells & Biology
  • About our Cells. New Cell Structure observations have been added
    • The Cell Structure Observations has 6 new entries for:
      • Cell–cell contacts: Gap junctions visualized via connexin-43​
      • Peroxisomes visualized via peroxisomal membrane protein PMP34
      • Endosomes visualized via Ras-Related Protein Rab-5A
      • Plasma Membrane visualized via CAAX domain of K-Ras
      • Nucleolus visualized via nucleophosmin
      • Sarcomere visualized via Troponin I, slow skeletal muscle
  • ​Cell Research Projects. Two new entries have been added to Cell Research Projects.
 
Microscopy
  • ​Interactive Plotting. This deprecated page, which points to the same tool available directly in the 3D Cell Viewer, has been moved to News / Archived Content
  • Data Downloading. This page has several updates and a new layout. The bulk downloads section now has a total of 24,928 segmented cells across 7,059 full-field images of cells.
    • Programmatic access to our cell images & metadata
    • Download cell feature data
    • Download cell image data as ome-tif files
  • More...  
    • Methods for Microscopy. The methods page has been rewritten to make it more visually descriptive. It will be iteratively improved in the coming months.

​Modeling & Analysis  The Modeling & Analysis category 5 new major content pages and 2 new landing pages.
News  ​We created this new top-level menu category to clarify navigation on allencell.org.​​
  • Archived Content. Content from retired pages remains available here.
    • The Interactive Plotting Tool page moved from ../Microscopy/ into Archived Content.
    • The Cell Variation Analyses page moved from ../Modeling&Analysis/ into Archived Content.
    • The Integrated Cell Models page moved from ../Modeling&Analysis/ into Archived Content.

April 5, 2018 update

The allencell.org website is undergoing a major reorganization to improve usability. These changes will be completed by April 5, 2018, and will be listed here as they occur.
​
Detailed updates to allencell.org include:

Home (now accessed via the Allen Cell Explorer logo)
  • Highlights text descriptions reduced.
​​
About A page has moved here from another part of the site.
  • What we do. This page, formerly at Methods / Institute Workflow has moved here and changed names to become About / What we do. The content is unchanged, but we plan to update information on this page later this month.
​
Cells & Biology This top-level menu category has changed names from Use our Cells to Cells & Biology to clarify navigation on allencell.org.
Content from the two pages from this top-level menu category, which were the Cell Catalog and the Cell Image Gallery can still be found under this new name Cells & Biology along with many new and reorganized pages.
  • The menu category, now called Cells & Biology has moved leftward next to the About menu category.
  • About our Cells. A new page called About our Cells organizes high-level articles about human induced pluripotent stem cell biology from the former Getting to Know the Cells page together with the per-structure Cell Structure Observations and Cell Catalog QuickView pages
    • A new page called hiPS Cell Biology Overview has short articles (formerly found in Research Progress / Cell Stories / Getting To Know The Cells) describing hIPS cells & what we have learned by growing, manipulating & imaging them.
    • The Cell Structure Observations blog has moved here. It was formerly under Research Progress/Cell Stories
    • The Cell Image Gallery is now called Cell Catalog QuickView and is a subcategory of a new page called About our Cells
  • Cell Catalog. The Cell Catalog remains unchanged at Cells & Biology / Cell Catalog
  • Genomics. A new page called Genomics added where you can explore & download genomics & transcriptomics data.
  • Cell Research Projects. A new page called Cell Research Projects collects observations we've made during human induced pluripotent stem cell biology experiments. Many articles formerly categorized under the former Getting to Know the Cells page can be found here:
  • More...  A new submenu Cells & Biology / More... holds four pages of material useful for researchers.
​
​Research Progress Content from this top-level menu category has moved into 5 new locations to make it easier for new visitors to find. This page has since been removed.  
  • Cell Stories. This submenu has been moved to become Cells & Biology / About our Cells
    • Getting to Know the Cells. The content from this page has moved into either Cells & Biology / About our Cells or Cells & Biology / Research Projects to make it easier to find. This page has since been removed.
    • Cell Structure Observations. This page has moved to Cells & Biology / Cell Structure Observations.
    • Extracting Information. The content from this page has moved to Microscopy / Research Projects.
  • Cell Variation Analysis. This page has moved to become Modeling / Cell Variation Analysis
  • Publications. This page has moved to become News / Collected Content / Publications Collected.
    • Further descriptions posted by April 5

Tools & Data This page is now called Microscopy

Microscopy. This top-level menu category has changed names from Tools & Data to Microscopy to clarify navigation on allencell.org.
Content from the four pages from this top-level menu category, which were the 3D Cell Viewer, Interactive Plotting, Data Downloads can still be found under this new name Microscopy along with many new and reorganized pages.
  • Data Downloading. We have collapsed the two pages found under Data Downloads into one new page called Data Downloading.
    • Feature Analysis Data Downloads. This content has moved to / Microscopy / Data Downloading.
    • Image Data Downloads. This content has moved to /Microscopy / Data Downloading.
  • Microscopy Research Projects. A new page called Microscopy Research Projects describes outcomes of projects to improve cell imaging. An article formerly categorized under the former Getting to Know the Cells page can be found here:
  • More...  A new submenu Microscopy / More... holds four pages of material useful for researchers.

Modeling. This page is now called Modeling & Analysis

Modeling & Analysis. This top-level menu category has changed names from Modeling to Modeling & Analysis to clarify navigation on allencell.org. 
Content from the one page from this top-level menu category, called Integrated Cell Models can still be found under this new name Modeling & Analysis along with another page which has moved into this category.
  • Cell Variation Analysis. This page has moved to become Modeling / Cell Variation Analysis
  • More...  A new submenu Modeling & Analysis / More... holds four pages of material useful for researchers.

News. ​We created this new top-level menu category to clarify navigation on allencell.org.
  • News Feed. This page has changed names from News to subdivide the News category and to clarify navigation on allencell.org.
  • Collected Content. Content from retired pages remains available here.
    • ​Publications Collected. This page has changed names from Publications. It provides a comprehensive list of scientific publications collected from each menu category.
    • Tutorials & Videos Collected. A comprehensive list of written tutorials & instructional videos collected from each menu category.
  • Archived Content. Content from retired pages remains available here.
    • The Detailed Methods page moved into Archived Content.
    • A Glossary of Cell Feature Analysis Terms was moved from the Feature Analysis Downloads page into Archived Content.

Use our Cells This page is now called Cells & Biology
Content from the two pages from this top-level menu category, which were the Cell Catalog and the Cell Image Gallery can still be found under the new name Cells & Biology along with many new and reorganized pages as described above in the Cells & Biology Site Update description.

Methods
  • Institute Workflow. This page, formerly at Methods / Institute Workflow has moved here and changed names to become About / What we do. The content is unchanged, but we plan to update information on this page later this month.

March 6, 2017 update

Only minor changes as we get ready for major updates in late April, but a great new Instructional Video added!
​
Other updates to allencell.org include:

Home (now accessed via the Allen Cell Explorer logo)
  • Highlights. 
    • ​Highlights have been added or removed:
      • added announcement of our 2nd Allen Cell Methods video released
      • older Highlights content removed (Biophysical Society announcement & Cell Catalog tutorial removed)
​
About 
This new top-level Overview of the Allen Cell Explorer website section moved here from the Home page to the About page

February 5, 2018 update

The Home button has been removed to simplify the interface. The Allen Cell Explorer Logo in the upper left will take you to allencell.org/, which is the Home page.
​
Other updates to allencell.org include:

Home (now accessed via the Allen Cell Explorer logo)
  • Highlights. 
    • ​Highlights have been added or removed:
      • added highlight to announce our booth and presentations at the Biophysical Society Annual Meeting 2018
      • added announcement of our 1st Allen Cell Methods video released
      • older Highlights content removed (November's release of the Molecular Biology of the Cell paper)
​
About 
  • News. Two new articles were added.
    • to announce our booth and presentations at the Biophysical Society Annual Meeting 2018
    • ​1st video in a new series of Allen Cell Methods released: Single cell passaging human iPS cells released
  • Tutorials. A new video is available
    • Megan Riel-Mehan represents the Animated Cell group to present an overview of several major upgrades and an easier to use interface for the 3D Cell Viewer tool.

Methods A new page called Instructional Videos has been added to the Methods menu.

December 5, 2017 update

The 3D Cell Viewer user-interface has many new features and is easier to use– a video, our second tutorial, highlights these details. Over 10,000 new cell images have been added to the publicly available data, and a new Highlights section has been added to the Home page to make it easier to learn about new items on allencell.org!
​
Other updates to allencell.org include:

Home
  • Highlights. This new section at the top of the Home page showcases big news about the institute and major updates made to allencell.org, it will alert you to exciting changes and major new data, tools or information available on allencell.org. 
    • ​Highlights have been added for
      • November's release of the Molecular Biology of the Cell paper
      • The new Cell Catalog tutorial video
      • The new 3D Cell Viewer tutorial video
  • Overview of the Allen Cell Explorer website section moved from the Home page to the About page
​
About 
This new top-level Overview of the Allen Cell Explorer website section moved here from the Home page to the About page
​Research Updates
  • Publications. Two new papers added to the Preprint section.
    • Building a 3D Integrated Cell
    • Three dimensional cross-modal image inference: label-free methods for subcellular structure prediction

Cells ​This page is now called Use our Cells

Use our Cells 
This top-level menu category has changed names from Cells to Use our Cells to clarify navigation on allencell.org

Tools & Data
  • 3D Cell Viewer. Over 10,000 new cells & improved user interface are now available.
    • The new viewer includes a 2D mode to scroll up and down through Z-stacks (or in the X and Y planes)
    • Many other major improvements have been made which are overviewed in the 3D Cell Viewer tutorial described above.
  • ​Interactive Plotting. This page has been deprecated and now points to the same tool available directly in the 3D Cell Viewer.

November 1, 2017 update

Our article Systematic gene tagging using CRISPR/Cas9 in human stem cells to illuminate cell organization has been published in final form in Molecular Biology of the Cell.
To make it easier to navigate this website, allencell.org, a new top-level menu category named "About" has been added. Pages formerly found under "Home" have been moved into this "About" category and the names of some pages have changed as detailed below. The FAQs page has moved from Methods to this new About category.
​
Other updates to allencell.org include:

Home
​About 
This new top-level menu category was created to simplify navigation on allencell.org
  • Site Updates. This page moved from under Home into this new About category (formerly called "What's New").
  • News. This page moved from under Home into this new About category.
    • An article about the Allen Institute for Cell Science booth, posters, and presentations at the 2017 ASCB | EMBO Meeting​ in Philadelphia is available. 
  • Tutorials. This page moved from under Home into this new About category. 
  • FAQs. This page moved from under Methods into this new About category. 
  • < AllenInstitute.org >. This link has moved from under Home into this new About category. 

Research Updates
  • Publications. An article has been published in final form with a PDF provided and a new section called "Preprinted versions" has been added.
    • Systematic gene tagging using CRISPR/Cas9 in human stem cells to illuminate cell organization
      The early-publication link to the Molecular Biology of the Cell (MBoC) article has been replaced by the final publication link.
    • A new section called "Preprinted Versions" has been added and two preprint articles have been moved into this category.

Methods
  • FAQs. This page has moved to the new About category. ​

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.
​
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
    • Allen Cell Explorer Tutorial: Navigating the Cell Catalog released
    • 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.
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