Find us at booth #311 in the exhibitor hall to:
- Speak with Allen Institute scientists about their presentations and posters at BPS 2018
- Learn about the mission of the Allen Institute for Cell Science and how to access our data on allencell.org
- Experience a demonstration of our data in virtual reality, daily from 11am - 1pm
- Hear about our CellProfiler collaboration with the Broad Institute to allow support for 3D volumetric datasets, daily at 10:30am and 4pm
Studying Stem Cell Organization Using "Label-Free" Methods and a Novel Generative Adversarial Model
Session: Computational Methods and Bioinformatics
Session Co-Chair: Molly Maleckar
Session Date & Time: Sunday, February 18, 4:00-6:00pm
Location: Esplanade Room 155
Presentation Date & Time: Sunday, February 18, 5:30pm
Presenter: Molly Maleckar
An integrated representation of the cell and subcellular structures would enhance understanding of cellular organization and how it produces characteristic phenotypes and changes as cells progress through the cell cycle, differentiate and otherwise change state, offering key insight into cells’ function. Fluorescence microscopy allows the imaging of labeled cellular components; however, current methodology limits the number of fluorescent tags that can be imaged simultaneously without gross cellular perturbations from tagging and imaging. To address this, we developed two deep learning tools: (a) a “label-free” method to predict fluorescently labeled structures patterns solely from 3D transmitted light microscopy images, and (b) a conditional 3D model of cell organization (the “Integrated Cell”) to predict the integrated location of cellular organelles from high replicate fluorescent microscopy images. In combination, the result is 3D integrated representations of cellular organization. In initial evaluation of model performance, we see excellent correspondence for several well-stereotyped intracellular structures. Ongoing work includes expanding predictions to several additional intracellular structures, increasing image resolution, and enhancing model interpretability.
Subgroup: Cell Biophysics
Date & Time: Saturday, February 17, 10:00am-12:00pm
Location: Esplanade Room 155
Speaker: Rick Horwitz, "The Allen Institute for Cell Science - creating a high dimensional cellular 'state space'"
Modern cell biology has made great strides in understanding cell structure and function. As with any engineering problem, however, there is a third important aspect that needs to be understood besides structure and function, and that is assembly. How are the complex three-dimensional structures found within the cell specified by a one-dimensional genome? In this session we will explore the mechanisms by which cellular structures are determined and regulated. Because this question lies at the interface of biology and physics, this Building the Cell session will be highly interdisciplinary with speakers whose interests range from physics and mathematical modeling to biochemistry and cell biology.
Exhibitor Presentation: The Allen Institute for Cell Science -- Resources to Empower Your Research
Date & Time: Sunday, February 18, 2:30-4:00pm
Location: Room 6
Speakers: Allen Institute for Cell Science team
In this presentation, the Allen Institute for Cell Science team will introduce you to the publicly available cell lines, observations, imaging and computational methods and tools, and the data produced by the Institute. We will discuss our legacy collection of endogenous fluorescently tagged human inducedpluripotent stem cell lines highlighting key intracellular structures, and how we image our cells in our high-replicate microscopy pipeline, that includes automated cell culture and imaging using spinning disk microscopy. We will also discuss our workflow quality control criteria, the methods developed to ensure day-to-day consistency between data sets, and how alternate pipeline modes may offer the flexibility to evaluate new assays and imaging technologies.
Monday, February 19
1699/B608 Novel Tools for Analyzing the Three-Dimensional Cellular Shape Space
L3652/LB98 Assessing Performance in a Novel Conditional Model of Cell Organization
Tuesday, February 20
2650/B666 Quantitative Microscopy Pipeline for Building a Model of the Human Cell