Changes in version 0.1.0 (2019-09-17):

+ initial commit 

Changes in version 0.2.0 (2019-11-28):

+ The functions calculateSummary, plotCellCounts, and plotDist have been added 

Changes in version 0.3.0 (2021-05-07):

+ Added helper functions for spillover correction
+ Removed redundant functions

Changes in version 0.3.1 (2021-05-15):

+ readSCEfromTXT accepts list and path

Changes in version 0.3.2 (2021-05-16):

+ adjusted plotSpotHeatmap function and unit test

Changes in version 0.3.3 (2021-05-17):

+ unit tests for binAcrossPixels

Changes in version 0.3.4 (2021-05-18):

+ added readImagefromTXT function and tests

Changes in version 0.3.5 (2021-05-20):

+ unit tests and docs for filterPixels

Changes in version 0.3.6 (2021-06-04):

+ added read_steinbock function, docs and tests

Changes in version 0.3.7 (2021-06-14):

+ added read_cpout function, docs and tests

Changes in version 0.3.8 (2021-06-30):

+ Adjusted default parameters for read_steinbock function
+ Added updated test data

Changes in version 0.3.9 (2021-07-29):

+ Added buildSpatialGraph function
+ Added plotSpatial function
+ Added aggregateNeighbors function

Changes in version 0.3.10 (2021-08-18):

+ Added countInteractions function
+ Added testInteractions function

Changes in version 0.3.11 (2021-08-19):

+ Added flip_x, flip_y argument for plotSpatial function
+ readSCEfromTXT does not require spot names anymore
+ knn graph construction can be pruned by distance
+ added

Changes in version 0.3.12 (2021-09-01):

+ clean up for Bioconductor submission

Changes in version 0.99.0 (2021-09-14):

+ Bioconductor submission

Changes in version 0.99.7 (2021-10-10):

+ Added all unit tests
+ Fixed read_steinbock x/y axis defaults

Changes in version 0.99.8 (2021-10-11):

+ Added patch detection method

Changes in version 0.99.9 (2021-10-22):

+ Removed certain unit tests for 64-bit windows

Changes in version 1.1.1 (2021-11-16):

+ Bug fix in testInteractions: consider now all possible combinations of cell types

Changes in version 1.1.2 (2021-11-28):

+ Moved all helper functions to single script

Changes in version 1.1.3 (2021-12-15):

+ Bug fix: divide number of interactions by total number of cells for classic and patch interaction counting

Changes in version 1.1.4 (2021-12-23):

+ Added option to restrict the maximum distance between neighbors in delaunay triangulation

Changes in version 1.1.5 (2022-01-07):

+ More specific access of metal tags

Changes in version 1.1.6 (2022-01-12):

+ Bug fix: correctly index graphs when reading in steinbock data

Changes in version 1.1.7 (2022-03-30):

+ readSCEfromTXT: only read in last metal occurrence in .txt file name

Changes in version 1.1.8 (2022-04-03):

+ Adjusted read_cpout function to newest pipeline

Changes in version 1.1.9 (2022-04-19):

+ Bug fix: patchDetection now works on SpatialExperiment object
+ Fix for release

Changes in version 1.3.1 (2022-04-28):

+ Bug fix: avoid using factors in testInteraction function for group_by

Changes in version 1.3.2 (2022-05-30):

+ Bug fix: avoid duplication of metadata entries

Changes in version 1.3.3 (2022-06-03):

+ Bug fix: specify the number of nodes in patchDetection function

Changes in version 1.3.4 (2022-06-14):

+ Avoid duplicated columns when generating nodes for plotSpatial

Changes in version 1.3.5 (2022-06-15):

+ Added three spatial context functions

Changes in version 1.3.6 (2022-07-28):

+ new function to measure size of patch

Changes in version 1.3.7 (2022-08-11)

+ new function to measure minimal distances to cells of interest

Changes in version 1.3.8 (2022-10-13)

+ exclude a single validity check to to class changes in the ggraph package

Changes in version 1.3.9 (2022-10-14)

+ new function for spatial community detection

Changes in version 1.3.10 (2022-10-22)

+ fix axis.ratio to 1 in plotSpatial function and set scales = "fixed"

Changes in version 1.5.1 (2022-11-22)

+ fix axis.ratio to 1 in plotSpatial function and set scales = "fixed"

Changes in version 1.5.2 (2022-11-23)

+ Bug fix minDistToCells: return NA when all cells of an image belong to a patch

Changes in version 1.5.3 (2023-03-23)

+ Replaced merge function by left_join as safety measure

Changes in version 1.5.4 (2023-04-04)

+ Added option to get permutation counts returned from testInteractions

Changes in version 1.5.5 (2023-04-20)

+ Bug fix: in corner cases, levels of the permuted factors in the testInteractions function do not match the baseline.
+ Bug fix: testInteractions now works for cells that are not ordered by grouping level
+ Added explicitly message for some functions that the output is ordered by image

Changes in version 1.7.1 (2023-06-07)

+ More info on reproducibility using detectCommunity

Changes in version 1.7.3 (2023-06-20)

+ More info on reproducibility using testInteractions

Changes in version 1.7.4 (2023-08-09)

+ Bug fix: correctly setting the "aspect.ratio" argument in plotSpatial to fix the physical units of the x- and y-axis

Changes in version 1.7.5 (2023-09-14)

+ Added more internal validity checks for 'read_steinbock'
+ Changed the way messages in vroom are silenced
+ Stop allowing Object numbers to be different between intensities and regionprops
+ Stop allowing missing files in regionprops and neighbors 

Changes in version 1.7.6 (2023-09-26)

+ Updated example data in "inst" to newest version

Changes in version 1.7.7 (2023-10-02)

+ Bug fix: in rare cases the testInteractions p-values were not correctly computed due to machine precision issues

Changes in version 1.7.8 (2023-10-19)

+ spatialCoords are not initialised with rownames anymore

Changes in version 1.9.1 (2023-11-20)

+ Switched from aes_ to .data
+ Initialise SPE and SCE objects with colnames
+ Additional test within binAcrossPixels

Changes in version 1.9.2 (2023-12-14)

+ maintainer change

Changes in version 1.11.1 (2024-10-03)

+ fixed BiocNeighbors error for DFrame type data

Changes in version 1.11.2 (2024-10-08)

+ fixed testInteraction and countInteraction tests due to machine precision issues

Changes in version 1.11.3 (2024-10-25)

+ fixed testdetectCommunity function

Changes in version 1.11.4 (2024-10-28)

+ changed testdetectCommunity function for group_by parameter

Changes in version 1.15.1

+ Replaced minDistToCells function with distToCells function

Changes in version 1.15.2 (2025-06-18)

+ Added "interaction" method to countInteractions and testInteractions
+ Added plotInteractions function

Changes in version 1.15.3 (2025-09-26)

+ Added general zscore output to 'testInteractions()'
+ Changed name "histocat" method to "conditional" method in countInteractions and testInteractions

Changes in version 1.15.4 (2025-10-08)

+ added readImagefromTIFF function and tests

Changes in version 1.15.5 (2025-10-20)

+ fixed machine imprecision in tests
+ fixed test_plotSpatialContext

Changes in version 1.17.1 (2026-03-30)

+ update function page/vignette

Changes in version 1.17.2 (2026-04-24)

+ Replaced deprecated aggregateAcrossCells function from scuttle package with scrapper implementation

Changes in version 1.19.1 (2026-05-08)

# fixed bug in plotSpotHeatmap function that had also affected RELEASE_3_23