Version 0.3.3

• Fix access to find_common_prefix in analysis app (#56)

Version 0.3.2

• Fix spatial map viewer to work with older composite images that are missing ImageDescription (#52)
• Update tests to work with testthat 3.1.

Version 0.3.1

Spatial map viewer:

• Remove a left-over debugging command.

Version 0.3.0

Mean of top 20 / bottom 10 addin:

• New addin helps to evaluate whether the staining quality is
  likely to produce good unmixing. See
  https://akoyabio.github.io/phenoptrReports/articles/top_20_bottom_10_report.html
  for details.

Staining consistency report:

• New addin creates a report showing mean expression of a selected marker
  across multiple samples.

Analysis addin:

• Fix problem computing mean expression for phenotypes with formulas
  in their definition #47
• Allow selecting (and reporting on) multiple score summary files #49
• Tabs with H-Score results include the scored marker name
  (in support of #49)

Spatial map viewer:

• Add support for selecting the desired view when the exported
  composite files contain multiple views.

Consolidate and summarize addin:

• Add a dummy Phenotype column if none is present #48

Merge addin:

• Read files to merge into memory and write once, instead of appending

Component levels report:

• Works correctly when "Export data from pairs plots" is checked #50

Version 0.2.13

Analysis addin:

• Fix problems with chart generation #46
• If there is only one Slide ID, don't offer to remove it as a prefix #46

Version 0.2.12

Fix a critical bug in the consolidate and summarize addin.

Version 0.2.11

Consolidate and summarize addin:

• Add support for reading (and saving) only fields needed in phenoptrReports.

Analysis addin:

• Preserve (or recreate) TMA information in the analysis output files.
• Only read cell seg fields needed for the analysis.
• Fix network file paths in Script.R.

Component levels report:

• Fix histograms to work with more than 11 components.
• Omit pairs plots with more than 10 components.
• Add correlation heatmaps for each file

Misc:

• Update to work with multi-schema phenotypes
• Fix report generation to work when paths contain spaces
• Require R 4.0.0 or higher for compatibility with latest rtree

Version 0.2.10

Consolidate and summarize addin:

• Reduce memory use to allow consolidation of larger files

Bug fixes:

• Nearest neighbor and count within summaries work correctly if detailed data is not requested.
• Correctly double-escape all backslashes in the slide id prefix.
• Improved error checks and error messages

Version 0.2.9

Analysis addin:

• Nearest neighbors and count within are computed per tissue category and for all cells in any included category (#39).
• Include expression-based phenotype columns and measured expression columns in count_within.txt and nearest_neighbors.txt (#36).
• Output has nicer names for expression-based phenotypes (#36).

Spatial map viewer addin:

• Fix "Save all" to work on a Mac

Version 0.2.8

Analysis addin:

• Remove summary lines from the Count Within worksheet, they are not correct (#35)!

Spatial map viewer addin:

• For the usual use where the client browser is running on the user's computer, the "Save all" saves directly to the local file system without creating an intermediate zip file. This is faster and avoids transfer of a potentially large zip file.

Misc:

• Fix to work correctly with dplyr 1.0.0.