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SMARTR 0.0.0.9000

  • First release of SMARTR

SMARTR 1.0.0

  • Major change in the way area/volume of regions is calculated to account for bug in underlying atlas in wholebrain that pulls the wrong region registration outlines for certain subregions. Specifically, areas such as the DG-sg and DG-mo are represented twice in the same atlas plate when the hippocampus curves rostral-caudally. Previously only one of the two subregion outlines were used to calculate area, which should now be fixed.
  • Change in the exclude_anatomy, get_registered_volumes, and normalize_cell_counts functions to include a simplify_keywords parameter which automatically re categorizes subregions to their major parent regions based on specific keywords.
  • Modified the normalize_cell_counts and combine_cell_counts function to also store counts and areas/volume by slice in the mouse and experiment objects, respectively. This allows for easy evaluation of the raw mapped dataset.
  • Our various analysis and visualization function are now compatible with the Kim lab's unified atlas. The unified atlas synthesizes label from two of the most highly used atlases --Franklin-Paxinos (FP) and the common coordinate framework (CCF) from the Allen Institute.Check out the various help pages for analysis and plotting functions to see which ones now includeontology as a relevant parameter. Simply change the value from allen to unified to process datasets using this ontology.
  • New function simplify_cell_count can process external datasets and simplify regions based on keywords. Simplification is based on user indicated atlas (allen or unified)

SMARTR 1.0.1

  • New function export_permutation_results reformats permutation results and saves it nicely for users.
  • Tables are now saved into an autocreated tables folder in the output directory for organization.
  • Added create_joined_networks and plot_joined_networks as as capability to visualize the overlapping edges in two networks with outer joined nodes. The capability to export a list of overlapping edges between the joined network is included as a parameter in create_joined_networks. See the documentation for more details.
  • Altered plot_correlation_heatmaps() function to automatically plot parent regions as subfacets