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Open AccessJournal ArticleDOI

Metadata matters: access to image data in the real world

TLDR
An open standard format for multidimensional microscopy image data is described and it is called on the community to use open image data standards and to insist that all imaging platforms support these file formats.
Abstract
Data sharing is important in the biological sciences to prevent duplication of effort, to promote scientific integrity, and to facilitate and disseminate scientific discovery. Sharing requires centralized repositories, and submission to and utility of these resources require common data formats. This is particularly challenging for multidimensional microscopy image data, which are acquired from a variety of platforms with a myriad of proprietary file formats (PFFs). In this paper, we describe an open standard format that we have developed for microscopy image data. We call on the community to use open image data standards and to insist that all imaging platforms support these file formats. This will build the foundation for an open image data repository.

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Citations
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Posted ContentDOI

Multiplexed chromatin imaging reveals predominantly pairwise long-range coordination between Drosophila Polycomb genes

TL;DR: Results indicate that long-range Pc interactions are temporally and spatially regulated during differentiation and development but do not involve clustering of multiple distant Pc genes.
Proceedings ArticleDOI

DeepLIIF: An Online Platform for Quantification of Clinical Pathology Slides

TL;DR: DeepLIIF as mentioned in this paper is a cloud-native platform for IHC scoring that supports more than 150 proprietary/non-proprietary input formats via the Bio-Formats standard, interactive ad-justment, visualization, and downloading of the IHC quan-tification results and the accompanying restained images.
Journal ArticleDOI

Complementary Use of Super-Resolution Imaging Modalities to Study the Nanoscale Architecture of Inhibitory Synapses

TL;DR: It is found that 3D-SIM and dSTORM provide complementary information regarding the distribution of NL2 at the inhibitory synapse, with NL2 forming nanoscale structures that have many similarities to gephyrin nanoscales architecture.
Posted ContentDOI

TFMLAB: a MATLAB toolbox for 4D traction force microscopy

TL;DR: TFMLAB integrates all the computational steps to compute active cellular forces from confocal microscopy images, including image processing, cell segmentation, image alignment, matrix displacement measurement and force recovery, and eases usability by means of interactive graphical user interfaces.
Journal ArticleDOI

Quantitative spatial evaluation of tumor-immune interactions in the immunotherapy setting of metastatic melanoma lymph nodes

TL;DR: In this paper , the authors applied multiplex immunofluorescence (MxIF) to spatially characterize tumor-immune interactions within the metastatic melanoma lymph node and applied a supervised classifier approach to resolve 10 distinct tumor, stromal and immune cell phenotypes and functional expression of PD1.
References
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Journal ArticleDOI

Genome-wide atlas of gene expression in the adult mouse brain

Ed S. Lein, +109 more
- 11 Jan 2007 - 
TL;DR: An anatomically comprehensive digital atlas containing the expression patterns of ∼20,000 genes in the adult mouse brain is described, providing an open, primary data resource for a wide variety of further studies concerning brain organization and function.
Journal ArticleDOI

Global Analysis of mRNA Localization Reveals a Prominent Role in Organizing Cellular Architecture and Function

TL;DR: A high-resolution fluorescent in situ hybridization procedure was developed and employed to comprehensively evaluate mRNA localization dynamics during early Drosophila embryogenesis, indicating major roles for mRNA localization in nucleating localized cellular machineries.
Journal ArticleDOI

The Zebrafish Information Network: the zebrafish model organism database

TL;DR: The Zebrafish Information Network (ZFIN) provides an integrated representation of mutants, genes, genetic markers, mapping panels, publications and community resources such as meeting announcements and contact information.
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