Computer vision for image-based transcriptomics.
TL;DR: The setup of the experimental pipeline for image-based transcriptomics is discussed, and the algorithms that were developed to extract, at high-throughput, robust multivariate feature sets of transcript molecule abundance, localization and patterning in tens of thousands of single cells across the transcriptome are described.
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About: This article is published in Methods. The article was published on 01 Sep 2015. and is currently open access.
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Figures
Figure 2 
Table 2: Suggested controls for the proper interpretation of single molecule measurements. 
Table 3: Time for image-based transcriptomics on ten 384-well plates to obtain results, whose quality appeared acceptable to us. Time estimates are based on our experience and depend upon the specific computational infrastructure. 
Figure 3 
Figure 4 
Table 1: Suggested controls for the detection of transcript molecules.
Citations
Data-analysis strategies for image-based cell profiling
Juan C. Caicedo,Sam Cooper,Florian Heigwer,Scott Warchal,Peng Qiu,Csaba Molnar,Aliaksei Vasilevich,Joseph Barry,Harmanjit Singh Bansal,Oren Kraus,Mathias Wawer,Lassi Paavolainen,Markus D. Herrmann,Mohammad Hossein Rohban,Jane Hung,Jane Hung,Holger Hennig,John Concannon,Ian Smith,Paul A. Clemons,Shantanu Singh,Paul Rees,Paul Rees,Peter Horvath,Peter Horvath,Roger G. Linington,Anne E. Carpenter +26 more
TL;DR: The steps required to create high-quality image-based (i.e., morphological) profiles from a collection of microscopy images are introduced and techniques that have proven useful in each stage of the data analysis process are recommended on the basis of the experience of 20 laboratories worldwide that are refining their image- based cell-profiling methodologies.
MIGA2 Links Mitochondria, the ER, and Lipid Droplets and Promotes De Novo Lipogenesis in Adipocytes
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Patterns of Early p21 Dynamics Determine Proliferation-Senescence Cell Fate after Chemotherapy
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A Systems-Level Study Reveals Regulators of Membrane-less Organelles in Human Cells.
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