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This package provides scripts to reproduce the analysis pipelines described in the article `Temporal integration of auxin information for the regulation of patterning <https://www.biorxiv.org/content/10.1101/469718v2>`_ and used to reconstruct population averages of Shoot Apical Meristems (SAM) of *Arabidopsis thaliana* with quantitative gene expression and hormonal signal 2D maps. It essentially gives access to two major quantitative image analysis and geometrical interpretation pipelines:
| **Image quantification & alignment** | Starting from microscopy acquisitions (CZI) of SAMs expressing an Auxin sensor (DII) and a CLV3 fluorescent reporter, this pipeline quantifies image intensity at cell level and performs an alignment of time lapse sequences into a common SAM reference frame. |
| **PIN image polarity analysis** | Using microscopy acquisitions of SAMs expressing a fluorescent auxin carrier (PIN) and a cell wall staining, this pipeline estimates polarities at cell level. It can also use the result from the previous pipeline to superimpose aligned auxin and PIN information.|
See the `documentation website <https://mosaic.gitlabpages.inria.fr/publications/sam_spaghetti/>`_ for installation guidelines, examples and tutorials.
This package provides scripts to reproduce the analysis pipelines described in the article `Temporal integration of auxin information for the regulation of patterning`_ and used to reconstruct population averages of Shoot Apical Meristems (SAM) of *Arabidopsis thaliana* with quantitative gene expression and hormonal signal 2D maps. It essentially gives access to two major quantitative image analysis and geometrical interpretation pipelines:
| **Image quantification & alignment** | Starting from microscopy acquisitions (CZI) of SAMs expressing an Auxin sensor (DII) and a CLV3 fluorescent reporter, this pipeline quantifies image intensity at cell level and performs an alignment of time lapse sequences into a common SAM reference frame. |
| **PIN image polarity analysis** | Using microscopy acquisitions of SAMs expressing a fluorescent auxin carrier (PIN) and a cell wall staining, this pipeline estimates polarities at cell level. It can also use the result from the previous pipeline to superimpose aligned auxin and PIN information.|
