count_within_manyin support of phenoptrReports.
count_withindoes not count self when ‘from’ and ‘to’ phenotypes are the same.
field_column(moved from phenoptrReports) and
compute_all_nearest_distanceto recognize “Annotation ID” as a field name.
spatial_distribution_reportto work with consolidated data from
square mmto match inForm output.
spatial_distribution_reportworks correctly with cell seg data in microns. To do so, it requires a component data file for the target field. Image dimensions are taken from that file.
count_touching_cellsworks correctly when cell seg data is in microns.
count_withinwon’t complain if the data doesn’t have a
parse_phenotypesfunction simplifies creation of selectors for
select_rowsrecognizes the column format of phenotype-per-marker data.
NAselector as “select all”. This is helpful in lists of selectors.
read_cell_seg_dataattempts to skip microns conversion if it was already done.
count_touching_cellsto work with two-pixel-wide membrane map. #8
count_within_batchto work with cell seg files which don’t have
density_bandsto estimate cell density at a distance from a boundary.
subset_distance_matrixin a backwards-incompatible way. This was done to put the
csdparameter first, matching other functions with a
spatial_distribution_reportcreates an HTML report showing the location and nearest-neighbor relations of cells in a single field.
count_touching_cellsuses morphological analysis of nuclear and membrane segmentation maps to find touching cells of paired phenotypes.
read_componentsreads component image files.
count_within_batchcount the number of
fromcells having a
tocell within a given radius.
list_cell_seg_fileslists all cell seg data files in a folder.
NAvalues in distance columns of cell seg tables. Previously
NAvalues could cause the column to be read as character data.