Changes in version 1.18.1 (2026-05-08) o bug fix in usage of aggregateAcrossCells function Changes in version 1.17.2 (2026-04-24) o Replaced deprecated aggregateAcrossCells function from scuttle package with scrapper implementation Changes in version 1.17.1 (2026-03-30) o update function page/vignette Changes in version 1.15.5 (2025-10-20) o fixed machine imprecision in tests o fixed test_plotSpatialContext Changes in version 1.15.4 (2025-10-08) o added readImagefromTIFF function and tests Changes in version 1.15.3 (2025-09-26) o Added general zscore output to 'testInteractions()' o Changed name "histocat" method to "conditional" method in countInteractions and testInteractions Changes in version 1.15.2 (2025-06-18) o Added "interaction" method to countInteractions and testInteractions o Added plotInteractions function Changes in version 1.15.1 o Replaced minDistToCells function with distToCells function Changes in version 1.11.4 (2024-10-28) o changed testdetectCommunity function for group_by parameter Changes in version 1.11.3 (2024-10-25) o fixed testdetectCommunity function Changes in version 1.11.2 (2024-10-08) o fixed testInteraction and countInteraction tests due to machine precision issues Changes in version 1.11.1 (2024-10-03) o fixed BiocNeighbors error for DFrame type data Changes in version 1.9.2 (2023-12-14) o maintainer change Changes in version 1.9.1 (2023-11-20) o Switched from aes_ to .data o Initialise SPE and SCE objects with colnames o Additional test within binAcrossPixels Changes in version 1.7.8 (2023-10-19) o spatialCoords are not initialised with rownames anymore Changes in version 1.7.7 (2023-10-02) o Bug fix: in rare cases the testInteractions p-values were not correctly computed due to machine precision issues Changes in version 1.7.6 (2023-09-26) o Updated example data in "inst" to newest version Changes in version 1.7.5 (2023-09-14) o Added more internal validity checks for 'read_steinbock' o Changed the way messages in vroom are silenced o Stop allowing Object numbers to be different between intensities and regionprops o Stop allowing missing files in regionprops and neighbors Changes in version 1.7.4 (2023-08-09) o Bug fix: correctly setting the "aspect.ratio" argument in plotSpatial to fix the physical units of the x- and y-axis Changes in version 1.7.3 (2023-06-20) o More info on reproducibility using testInteractions Changes in version 1.7.1 (2023-06-07) o More info on reproducibility using detectCommunity Changes in version 1.5.5 (2023-04-20) o Bug fix: in corner cases, levels of the permuted factors in the testInteractions function do not match the baseline. o Bug fix: testInteractions now works for cells that are not ordered by grouping level o Added explicitly message for some functions that the output is ordered by image Changes in version 1.5.4 (2023-04-04) o Added option to get permutation counts returned from testInteractions Changes in version 1.5.3 (2023-03-23) o Replaced merge function by left_join as safety measure Changes in version 1.5.2 (2022-11-23) o Bug fix minDistToCells: return NA when all cells of an image belong to a patch Changes in version 1.5.1 (2022-11-22) o fix axis.ratio to 1 in plotSpatial function and set scales = "fixed" Changes in version 1.3.10 (2022-10-22) o fix axis.ratio to 1 in plotSpatial function and set scales = "fixed" Changes in version 1.3.9 (2022-10-14) o new function for spatial community detection Changes in version 1.3.8 (2022-10-13) o exclude a single validity check to to class changes in the ggraph package Changes in version 1.3.7 (2022-08-11) o new function to measure minimal distances to cells of interest Changes in version 1.3.6 (2022-07-28) o new function to measure size of patch Changes in version 1.3.5 (2022-06-15) o Added three spatial context functions Changes in version 1.3.4 (2022-06-14) o Avoid duplicated columns when generating nodes for plotSpatial Changes in version 1.3.3 (2022-06-03) o Bug fix: specify the number of nodes in patchDetection function Changes in version 1.3.2 (2022-05-30) o Bug fix: avoid duplication of metadata entries Changes in version 1.3.1 (2022-04-28) o Bug fix: avoid using factors in testInteraction function for group_by Changes in version 1.1.9 (2022-04-19) o Bug fix: patchDetection now works on SpatialExperiment object o Fix for release Changes in version 1.1.8 (2022-04-03) o Adjusted read_cpout function to newest pipeline Changes in version 1.1.7 (2022-03-30) o readSCEfromTXT: only read in last metal occurrence in .txt file name Changes in version 1.1.6 (2022-01-12) o Bug fix: correctly index graphs when reading in steinbock data Changes in version 1.1.5 (2022-01-07) o More specific access of metal tags Changes in version 1.1.4 (2021-12-23) o Added option to restrict the maximum distance between neighbors in delaunay triangulation Changes in version 1.1.3 (2021-12-15) o Bug fix: divide number of interactions by total number of cells for classic and patch interaction counting Changes in version 1.1.2 (2021-11-28) o Moved all helper functions to single script Changes in version 1.1.1 (2021-11-16) o Bug fix in testInteractions: consider now all possible combinations of cell types Changes in version 0.99.9 (2021-10-22) o Removed certain unit tests for 64-bit windows Changes in version 0.99.8 (2021-10-11) o Added patch detection method Changes in version 0.99.7 (2021-10-10) o Added all unit tests o Fixed read_steinbock x/y axis defaults Changes in version 0.99.0 (2021-09-14) o Bioconductor submission Changes in version 0.3.12 (2021-09-01) o clean up for Bioconductor submission Changes in version 0.3.11 (2021-08-19) o Added flip_x, flip_y argument for plotSpatial function o readSCEfromTXT does not require spot names anymore o knn graph construction can be pruned by distance o added Changes in version 0.3.10 (2021-08-18) o Added countInteractions function o Added testInteractions function Changes in version 0.3.9 (2021-07-29) o Added buildSpatialGraph function o Added plotSpatial function o Added aggregateNeighbors function Changes in version 0.3.8 (2021-06-30) o Adjusted default parameters for read_steinbock function o Added updated test data Changes in version 0.3.7 (2021-06-14) o added read_cpout function, docs and tests Changes in version 0.3.6 (2021-06-04) o added read_steinbock function, docs and tests Changes in version 0.3.5 (2021-05-20) o unit tests and docs for filterPixels Changes in version 0.3.4 (2021-05-18) o added readImagefromTXT function and tests Changes in version 0.3.3 (2021-05-17) o unit tests for binAcrossPixels Changes in version 0.3.2 (2021-05-16) o adjusted plotSpotHeatmap function and unit test Changes in version 0.3.1 (2021-05-15) o readSCEfromTXT accepts list and path Changes in version 0.3.0 (2021-05-07) o Added helper functions for spillover correction o Removed redundant functions Changes in version 0.2.0 (2019-11-28) o The functions calculateSummary, plotCellCounts, and plotDist have been added Changes in version 0.1.0 (2019-09-17) o initial commit