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import scimap as sm

Preprocessing: pp

Scimap provides a suite of tools to preprocess the data for subsequent analysis.

Function Short Description
sm.pp.mcmicro_to_scimap mcmicro output to scimap compatible object
sm.pp.rescale Manual/Auto gate based scaling of data
sm.pp.combat Batch correction tool

Tools: tl Probability distribution based cell phenotyping Cluster or sub-cluster single-cells using a variety of algorithms Dimensionality Reduction using UMAP Compute foldchange in phenotypes between samples/ROIs Computes nearest distance between all phenotypes for every cell cell–cell interactions analysis Distribution of cell-types with local neighborhood Latent Dirichlet Allocation (LDA) modelling for spatial motifs Distribution of spatial expression with local neighborhood Distribution of spatial expression with local neighborhood Scoring proximity between user defined cell types Aggregates of cell-types with local neighborhood Search for similar looking regions within and across images

Plotting: pl Opens the image with overlays on a napari browser Add ROI's with napari browser Overlays gating positivity on the image for manual gating Distribution plot of a given marker 2D density plotting of marker expression Meta function that outputs umap, heatmap and ranked makers for each group Overlays markers on UMAP vizualize foldchange in phenotypes between samples/ROIs Scatter plots of spatially resolved data Visualize distance between phenotypes Heatmap of cell–cell interaction analysis Bar plot of the derived Spatial Proximity Scores Generate a stacked barplot from any two columns of categorical data Generate a pieplot of cell-type proportion or any categorical data Generate a voronoi diagram and color it with categorical data

Helper Functions: hl

sm.hl.classify Quickly classify cells based on pos/negativity of list of markers
sm.hl.rename Quickly rename values within columns based on dict mapping
sm.hl.addROI_omero Add ROI's extracted from Omero to Scimap object
sm.hl.dropFeatures Handy Function to subset the adata object
sm.hl.animate Create a animated scatter plot of embedding -> physical location
sm.hl.scimap_to_csv Export scimap object to CSV