Open for (Cell) Science tutorials

​OPEN FOR (CELL) SCIENCE TUTORIAL
​3D Cell Visualization Tools
​We are developing new approaches to render volumes for visualizing cell images. The following would be demonstrated:
  • Advanced GPU Accelerated Volume Explorer (AGAVE), an open-source visualization software, which can be downloaded to use on your image files
  • Cell Feature Explorer, a web app allows you to explore, sort, and download our imaging data for your own modeling, analysis, or machine learning tasks
  • Simularium, an online tool to share, visualize, and interrogate biological simulations
Presented by Kimberly R. Metzler, PhD, and Kaytlyn Gerbin, PhD.
​OPEN FOR (CELL) SCIENCE TUTORIAL
Allen Cell Collection
The Allen Institute for Cell Science is creating the Allen Cell Collection, a collection of fluorescent protein-tagged hiPS cell lines listed in the Allen Cell Catalog with the objective to illuminate cell organization and enable observation of cellular behavior from a structural perspective. 

We have made all of these cell lines and plasmids available to use in the lab, in stem cell cores, or by industry partners.
​
Presented by Kimberly R. Metzler, PhD.
OPEN FOR (CELL) SCIENCE TUTORIAL
Allen Cell & Structure Segmenter
The Allen Cell and Structure Segmenter is a Python-based open source toolkit that enables users to combine classic image segmentation with iterative deep learning workflows. Two straightforward “human-in-the-loop” curation strategies convert a set of classic image segmentation workflow results into a set of 3D ground truth images for iterative model training without the need for manual painting in 3D.

This webinar will prepare you to use the Allen Cell and Structure Segmenter in your research to process 3D fluorescent images for quantitative analysis.

Presented by Kimberly R. Metzler, PhD, and Kaytlyn Gerbin, PhD.

Allen Cell Explorer tutorials

ALLEN CELL AND STRUCTURE SEGMENTER TUTORIAL 
Creating a new classic image segmentation workflow
​To assist biologists and computational scientists with using the Allen Cell Structure Segmenter, our Scientific Data Engineer, Ruian Yang, walks users through the steps to create a new classic segmentation workflow for 3D image processing and provides helpful tips throughout the demonstration.​
ALLEN CELL EXPLORER TUTORIAL 
Navigating the Cell Catalog
Explore our collection of fluorescently tagged human induced pluripotent stem cell lines as part of the Allen Cell Collection. These cell lines target key cellular structures and they are openly available to support your research.

​In this video tutorial, Allen Institute for Cell Science intern Rennie Dupar walks you through the cell lines, supporting data and images, and important resources.
ALLEN CELL EXPLORER TUTORIAL 
Navigating the 3D Cell Viewer
​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.

The 3D Cell Viewer is a tool in the Allen Cell Explorer for viewing thousands of 3D images of cellular structures and organelles.

The written tutorials offer a more detailed description of every button and option the 3D Cell Viewer provides.
More videos to come..

Archived

ALLEN CELL EXPLORER TUTORIAL
Navigating the Cell Catalog
Amanda Haupt represents the gene-editing team and walks you through the cell lines and supporting data available in the Cell Catalog, and how to obtain the lines for use in your labs.

​The Cell Catalog contains our completed cell lines, which are available through Coriell as part of the Allen Cell Collection. Click a cell line on the first page of the Cell Catalog to opens pages with supplemental material (data, images, videos) related to the rigorous testing and quality control steps each line has undergone.
Allen Institute for Cell Science is a part of the Allen Institute. The mission of the Allen Institute is to understand the principles that govern life, and to advance health. Our creative and multi-dimensional teams focus on answering some of the biggest questions in bioscience. We accelerate foundational research, catalyze bold ideas, develop tools and models, and openly share our science to make a broad, transformational impact on the world.
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