This repository contains code notebooks (Quarto and Python) associated with the research on PDGFR-B reactivity following brain ischemia.
Folders are listed in alphabetic order.
ProData: Contains processed data sets used for analysis and visualization. These data frames are generated from raw data available at the RawData folder, or the Open Science Framework (OSF) repository if the files are too heavy. The precise handling of the data is show in specific notebooks.
The notebooks are listed according to the suggested execution order to follow the research pipeline described in the research article (XXXXXX)
Confocal_40x_Pdgfrb_Morphology.qmd: Contains data handling and statistical modeling for the analysis features extracted with Confocal_40x_ROIs_Pdgfrb_MorphologicalAnalysis_skimage.py.
Confocal_40x_ROIs_Pdgfrb_MorphologicalAnalysis_skimage.py: Python script to extract morphological features from selected cells.
Widefield_5x_Shrinkage.qmd: Contains data handling and statistical modeling for the analysis of brain shrinkage.
Widefield_5x_Pdgfrb-IntDen.qmd: Contains data handling and statistical modeling for the analysis of PDGFR-β integrated density.
Widefield_5x_Pdgfrb-LowHigh.qmd: Contains data handling and statistical modeling for the proportion of reactive (PDGFR-β_high) cells in cortico-striatal lesions.
Widefield_5x_Pdgfrb-LowHigh_Str.qmd: Contains data handling and statistical modeling for the proportion of reactive (PDGFR-β_high) cells in striatal (only regions).
Widefield_5x_Gfap-IntDen.qmd: Contains data handling and statistical modeling for the analysis of GFAP integrated density.
Widefield_5x_Gfap-Convex.qmd: Contains data handling and statistical modeling for the analysis of GFAP convex hull in the ischemic hemisphere.
Widefield_5x_Pdgfrb-Gfap_Covariance.qmd: Contains data and point pattern analysis for PDGFR-β and its covariance for GFAP. This notebook process the data from cortico-striatal lesions.
Widefield_5x_Pdgfrb-Gfap_Covariance_Str.qmd: Contains data and point pattern analysis for PDGFR-β and its covariance for GFAP. This notebook process the data from striatal (only) lesions.
Widefield_10x_Pdgfrb-Gfap_Covariance.qmd: Contains data and point pattern analysis for PDGFR-β and its covariance for GFAP.
Widefield_10x_Klf4_Detections.qmd: Contains data and point pattern analysis for KLF4 spatial and intensity analysis.
Widefield_20x_Klf4_Detections.qmd: Contains data analysis for KLF4/PDGFR-β colocalization in defined ROIs.
.bib files These are files associated to each notebook containing cited bibliography. science.csl This files contains the Science Journal citation style implemented in the notebooks. Please note this is style is not associated to the journal the original research artiche is publish in.