Man pages for valeriabonapersona/abc4d
Analysis of Brain Cells in 4 Dimensions
| adapt_estimation_atlas | Adapt estimation atlas from Erö et al. to be used in the... |
| atlas_estimation | Atlas with estimation of number of cells per brain area by... |
| atlas_tree | Allen Brain Reference Atlas tree structure of brain areas. |
| calculate_density | Calculate density of active cells |
| categorize_strategy | Categorize the strategy of brain areas based on the... |
| cfos_expression_aba | Expression of cfos from Allen Brain Atlas API |
| clean_counts | Clean xyz coordinates of identified cells |
| example | Miniature example of whole-brain imaging data over time from... |
| find_all_children | Find smaller areas (children) of a larger brain area... |
| find_changed_strategy | Find brain areas that meet the criteria for analysis of... |
| find_children | Find smaller areas (children) of a larger brain area... |
| find_intercept | Function to find where an interpolated linear curve crosses a... |
| find_most_active | Find most active brain areas |
| find_parents | Find larger grouping areas (parents) of a smaller brain area... |
| from_aba_api_to_df | Convert data downloaded from Allen Brain Atlas API to a... |
| hello | Hello, World! |
| mask | Mask for data cleaning of whole-brain microscopy. |
| normalize | Normalize cell counts |
| order_brain_areas | Order time of activation of brain areas based on their... |
| pairwise_activation | Calculate pairwise activation across groups |
| plotting_all_coordinates_2d | Plot all combinations of xyz coordinates in 2D |
| plotting_coordinates_2d | Plot combinations of xyz coordinates in 2D |
| prepare_sim_weights | Prepare weights for simulation |
| preprocess_per_region | Normalize and scale for region-based analyses |
| remove_blinding | Remove (or scramble) blinding of your groups |
| samples_files_to_df | Merges in one data frame all the separate samples' files |
| sim_most_active | Simulate most active brain areas for one experiment |
| sim_most_active_one_batch | Simulate most active brain areas for one batch |
| specify_damage | Specify damaged areas per sample |
| summarize_per_region | Transform xyz coordinates data in a summary per brain region |
| voxelize | Voxelize xyz coordinates |
