Read and preprocess inForm data and image files

list_cell_seg_files

Find inForm data files.

read_cell_seg_data

Read and clean an inForm data file.

get_field_info

Read information about a field from a component image file.

read_components

Read a component TIFF file.

read_maps

Read an inForm segmentation map file.

parse_tissue_description

Parse the description tag of the tissue map image read from an inForm binary_seg_maps file

Compute and visualize spatial relationships between cells

find_nearest_distance

Nearest neighbor distances for each cell and phenotype.

compute_all_nearest_distance

Nearest neighbors from a file.

count_within

Count cells within a radius for a single field.

count_within_batch

Count cells within a radius for multiple tissue categories, phenotypes and fields.

count_touching_cells

Find and count touching cells for pairs of phenotypes.

spatial_distribution_report

Create a spatial distribution report.

Estimate cell density

density_bands

Estimate cell density in bands from a tissue boundary.

density_at_distance

Estimate cell density at distance from a tissue boundary.

Helpers

select_rows

Flexibly select rows of a data frame.

distance_matrix

Create a distance matrix from cell seg data.

plot_diverging

Plot a distance map using a diverging color scale with white at 0

subset_distance_matrix

Subset the rows and columns of a distance matrix.

Sample data

sample_cell_seg_data sample_cell_seg_path sample_cell_seg_folder

Sample cell segmentation data.