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02989nam a2200553Ia 4500 |
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10.1186-s12859-021-04302-5 |
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220427s2021 CNT 000 0 und d |
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|a 14712105 (ISSN)
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|a Matisse: a MATLAB-based analysis toolbox for in situ sequencing expression maps
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|b BioMed Central Ltd
|c 2021
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|z View Fulltext in Publisher
|u https://doi.org/10.1186/s12859-021-04302-5
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|a Background: A range of spatially resolved transcriptomic methods has recently emerged as a way to spatially characterize the molecular and cellular diversity of a tissue. As a consequence, an increasing number of computational techniques are developed to facilitate data analysis. There is also a need for versatile user friendly tools that can be used for a de novo exploration of datasets. Results: Here we present MATLAB-based Analysis toolbox for in situ sequencing (ISS) expression maps (Matisse). We demonstrate Matisse by characterizing the 2-dimensional spatial expression of 119 genes profiled in a mouse coronal section, exploring different levels of complexity. Additionally, in a comprehensive analysis, we further analyzed expression maps from a second technology, osmFISH, targeting a similar mouse brain region. Conclusion: Matisse proves to be a valuable tool for initial exploration of in situ sequencing datasets. The wide set of tools integrated allows for simple analysis, using the position of individual reads, up to more complex clustering and dimensional reduction approaches, taking cellular content into account. The toolbox can be used to analyze one or several samples at a time, even from different spatial technologies, and it includes different segmentation approaches that can be useful in the analysis of spatially resolved transcriptomic datasets. © 2021, The Author(s).
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|a Analysis toolbox
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|a animal
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|a animal experiment
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|a Animals
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|a article
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|a brain
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|a Brain
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|a Brain
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|a brain region
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|a Cellular diversity
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|a cluster analysis
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|a Cluster Analysis
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|a Comprehensive analysis
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|a Computational technique
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|a data analysis software
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|a Dimensional reduction
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|a gene expression
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|a In situ sequencing
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|a Initial exploration
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|a male
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|a Mammals
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|a Mice
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|a mouse
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|a nonhuman
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|a Probabilistic cell typing
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|a Spatial expressions
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|a Spatial technologies
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|a Spatially resolved
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|a Spatially resolved transcriptomics
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|a transcriptome
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|a Transcriptome
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|a transcriptomics
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|a Gyllborg, D.
|e author
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|a Marco Salas, S.
|e author
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|a Mattsson Langseth, C.
|e author
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|a Nilsson, M.
|e author
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| 773 |
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|t BMC Bioinformatics
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