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adapt_estimation_atlas()
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Adapt estimation atlas from Erö et al. to be used in the analysis |
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atlas_estimation
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Atlas with estimation of number of cells per brain area by Erö et al. |
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atlas_tree
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Allen Brain Reference Atlas tree structure of brain areas. |
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calculate_density()
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Calculate density of active cells |
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categorize_strategy()
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Categorize the strategy of brain areas based on the relationship between
median count of + cells and median of mean intensity of protein expression. |
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cfos_expression_aba
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Expression of cfos from Allen Brain Atlas API |
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clean_counts()
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Clean xyz coordinates of identified cells |
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example
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Miniature example of whole-brain imaging data over time from Bonapersona et al. |
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find_all_children()
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Find smaller areas (children) of a larger brain area categorization
(parent) in the Allen Brain Atlas. |
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find_changed_strategy()
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Find brain areas that meet the criteria for analysis of strategy across groups |
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find_children()
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Find smaller areas (children) of a larger brain area categorization
(parent) in the Allen Brain Atlas. |
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find_intercept()
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Function to find where an interpolated linear curve crosses a y value |
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find_most_active()
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Find most active brain areas |
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find_parents()
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Find larger grouping areas (parents) of a smaller brain area
(child) in the Allen Brain Atlas. |
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from_aba_api_to_df()
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Convert data downloaded from Allen Brain Atlas API to a dataframe |
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hello()
|
Hello, World! |
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mask
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Mask for data cleaning of whole-brain microscopy. |
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normalize()
|
Normalize cell counts |
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order_brain_areas()
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Order time of activation of brain areas based on their expression levels |
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pairwise_activation()
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Calculate pairwise activation across groups |
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plotting_all_coordinates_2d()
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Plot all combinations of xyz coordinates in 2D |
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plotting_coordinates_2d()
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Plot combinations of xyz coordinates in 2D |
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prepare_sim_weights()
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Prepare weights for simulation |
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preprocess_per_region()
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Normalize and scale for region-based analyses |
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remove_blinding()
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Remove (or scramble) blinding of your groups |
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samples_files_to_df()
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Merges in one data frame all the separate samples' files |
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sim_most_active()
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Simulate most active brain areas for one experiment |
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sim_most_active_one_batch()
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Simulate most active brain areas for one batch |
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specify_damage()
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Specify damaged areas per sample |
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summarize_per_region()
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Transform xyz coordinates data in a summary per brain region |
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voxelize()
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Voxelize xyz coordinates |