Open for (Cell) Science tutorials

Join us for a series of tutorials showcasing open resources from the Allen Cell Explorer. At these tutorials, learn how and why to integrate Allen Institute for Cell Science open cell lines and software tools into your research. Team members who worked on each resource will discuss the development process, use cases, and more.

3D Cell Visualization Tools

October 19, 2021 | 10:00-11:00am Pacific Time

Visualizing 3D cellular images and simulations: learn about AGAVE, Cell Feature Explorer, and Simularium

We are developing new approaches to render volumes for visualizing cell images. For example, by adopting approaches such as “cinematic rendering” techniques to cellular volumetric data, users can see fine details and interpret spatial relationships, even in a 2D static printed image. We will describe our open-source visualization software, Advanced GPU Accelerated Volume Explorer (AGAVE), which can be downloaded to use on your image files. We will also show how you can explore, sort, and download our imaging data in our Cell Feature Explorer for your own modeling, analysis, or machine learning tasks. In addition, we will show you how you can explore cell models in our online Simularium, a tool to share, visualize, and interrogate biological simulations. Presented by Kimberly R. Metzler, PhD, Senior Scientific Program Manager, and Kaytlyn Gerbin, PhD, Scientist.

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Allen Cell Collection

June 11, 2021 | 10:00-11:00am Pacific Time

Fluorescently-tagged human induced pluripotent stem cell (hiPSC) lines to investigate cell and nuclear organization in differentiation, disease, and regeneration

The Allen Institute for Cell Science is creating a collection of fluorescent protein-tagged hiPS cell lines with the objective to illuminate cell organization and enable observation of cellular behavior from a structural perspective. To date, the Allen Cell Collection consists of >40 edited lines with fluorescent tags labeling all the major cellular organelles, signaling molecules, cardiomyocyte-specific structures, phase transition markers, and transcription factors. We have also released a dCas9 line (dCas9-KRAB) which enables CRISPRi-mediated knockdown of target genes. 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, Senior Scientific Program Manager.

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Allen Cell and Structure Segmenter

September 21, 2021 | 10:00-11:00am Pacific Time

An open source tool for 3D segmentation of intracellular structures in fluorescence microscopy images

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. We developed a set of 20 classic image segmentation workflows that serve as a “lookup table” reference and starting point for users, and also made this available as a plugin for the Napari viewer. The iterative deep learning workflow can take over when the classic segmentation workflow is insufficient. 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, Senior Scientific Program Manager, and Kaytlyn Gerbin, PhD, Scientist.

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