scispace - formally typeset
Search or ask a question
Institution

Allen Institute for Cell Science

Facility
About: Allen Institute for Cell Science is a based out in . It is known for research contribution in the topics: Image segmentation & Population. The organization has 111 authors who have published 75 publications receiving 1906 citations.

Papers published on a yearly basis

Papers
More filters
Journal ArticleDOI
TL;DR: CellProfiler 3.0 is described, a new version of the software supporting both whole-volume and plane-wise analysis of three-dimensional image stacks, increasingly common in biomedical research.
Abstract: CellProfiler has enabled the scientific research community to create flexible, modular image analysis pipelines since its release in 2005. Here, we describe CellProfiler 3.0, a new version of the software supporting both whole-volume and plane-wise analysis of three-dimensional (3D) image stacks, increasingly common in biomedical research. CellProfiler's infrastructure is greatly improved, and we provide a protocol for cloud-based, large-scale image processing. New plugins enable running pretrained deep learning models on images. Designed by and for biologists, CellProfiler equips researchers with powerful computational tools via a well-documented user interface, empowering biologists in all fields to create quantitative, reproducible image analysis workflows.

1,466 citations

Journal ArticleDOI
TL;DR: A label-free method for predicting three-dimensional fluorescence directly from transmitted-light images is presented and it is demonstrated that it can be used to generate multi-structure, integrated images.
Abstract: Understanding cells as integrated systems is central to modern biology. Although fluorescence microscopy can resolve subcellular structure in living cells, it is expensive, is slow, and can damage cells. We present a label-free method for predicting three-dimensional fluorescence directly from transmitted-light images and demonstrate that it can be used to generate multi-structure, integrated images. The method can also predict immunofluorescence (IF) from electron micrograph (EM) inputs, extending the potential applications. Convolutional neural networks enable prediction of fluorescently labeled structures from three-dimensional time-lapse transmitted-light images. Applications include multiplexed long time-lapse imaging and prediction of fluorescence in electron micrographs.

351 citations

Journal ArticleDOI
TL;DR: The CellProfiler 4 as discussed by the authors is a new version of this software with expanded functionality based on user feedback, and it has made several user interface refinements to improve the usability of the software.
Abstract: Background Imaging data contains a substantial amount of information which can be difficult to evaluate by eye. With the expansion of high throughput microscopy methodologies producing increasingly large datasets, automated and objective analysis of the resulting images is essential to effectively extract biological information from this data. CellProfiler is a free, open source image analysis program which enables researchers to generate modular pipelines with which to process microscopy images into interpretable measurements. Results Herein we describe CellProfiler 4, a new version of this software with expanded functionality. Based on user feedback, we have made several user interface refinements to improve the usability of the software. We introduced new modules to expand the capabilities of the software. We also evaluated performance and made targeted optimizations to reduce the time and cost associated with running common large-scale analysis pipelines. Conclusions CellProfiler 4 provides significantly improved performance in complex workflows compared to previous versions. This release will ensure that researchers will have continued access to CellProfiler's powerful computational tools in the coming years.

268 citations

Posted ContentDOI
30 Jun 2021-bioRxiv
TL;DR: The CellProfiler 4 as mentioned in this paper is a new version of this software which has been ported to the Python 3 language based on user feedback, which has made several user interface refinements to improve the usability of the software.
Abstract: CellProfiler is a free, open source image analysis program which enables researchers to generate modular pipelines with which to process microscopy images into interpretable measurements. Here we describe CellProfiler 4, a new version of this software which has been ported to the Python 3 language. Based on user feedback, we have made several user interface refinements to improve the usability of the software. We introduced new modules to expand the capabilities of the software. We also evaluated performance and made targeted optimisations to reduce the time and cost associated with running common large-scale analysis pipelines. This release will ensure that researchers will have continued access to CellProfilers powerful computational tools in the coming years.

195 citations

Journal ArticleDOI
TL;DR: The generation of a collection of human induced pluripotent stem cell lines expressing endogenously GFP-tagged proteins using CRISPR/Cas9 methods is described and the genomic and cell biological data validating the GFP -tagged hiPSC lines are presented.
Abstract: We present a CRISPR/Cas9 genome-editing strategy to systematically tag endogenous proteins with fluorescent tags in human induced pluripotent stem cells (hiPSC). To date, we have generated multiple hiPSC lines with monoallelic green fluorescent protein tags labeling 10 proteins representing major cellular structures. The tagged proteins include alpha tubulin, beta actin, desmoplakin, fibrillarin, nuclear lamin B1, nonmuscle myosin heavy chain IIB, paxillin, Sec61 beta, tight junction protein ZO1, and Tom20. Our genome-editing methodology using Cas9/crRNA ribonuclear protein and donor plasmid coelectroporation, followed by fluorescence-based enrichment of edited cells, typically resulted in <0.1-4% homology-directed repair (HDR). Twenty-five percent of clones generated from each edited population were precisely edited. Furthermore, 92% (36/39) of expanded clonal lines displayed robust morphology, genomic stability, expression and localization of the tagged protein to the appropriate subcellular structure, pluripotency-marker expression, and multilineage differentiation. It is our conclusion that, if cell lines are confirmed to harbor an appropriate gene edit, pluripotency, differentiation potential, and genomic stability are typically maintained during the clonal line-generation process. The data described here reveal general trends that emerged from this systematic gene-tagging approach. Final clonal lines corresponding to each of the 10 cellular structures are now available to the research community.

171 citations


Authors

Showing all 111 results

Network Information
Related Institutions (5)
Howard Hughes Medical Institute
34.6K papers, 5.2M citations

85% related

Wellcome Trust Sanger Institute
9.6K papers, 1.2M citations

85% related

Salk Institute for Biological Studies
13.1K papers, 1.6M citations

85% related

Cold Spring Harbor Laboratory
6.6K papers, 1M citations

85% related

Broad Institute
11.6K papers, 1.5M citations

85% related

Performance
Metrics
No. of papers from the Institution in previous years
YearPapers
202115
202011
201915
201816
201715
20163