Man pages for jdknguyen/SMART
SMART (Semi-manual alignment to reference template): a pipeline for whole brain mapping projects
| brainmorph | Generate a brain morph plot *(W)* |
| cell_count_compilation | Compile cell counts from multiple brains. |
| cell_counter | Plate-by-plate cell counter for _segs_ object. |
| choice | Alignment choice game to align internal reference planes... |
| clean_duplicates | Duplicate cell cleanup *(W)* |
| concatenate | Concatenate multiple datasets |
| dot-onAttach | On attachment of SMART |
| filter_loop | Loop through reference slices |
| forward_warp | Forward warp back to atlas space |
| get_groups | Compile group data from individual brains. |
| get_rois | Get ROI data from a mapped wholebrain dataset. |
| get_savepaths | Automatically generates savepaths and save directories. |
| get_sunburst | Generate a sunburst plot using a forward warped dataset. |
| get_table | Create a data frame of left/right counts and their ratio of... |
| get_tree | Create a dataframe of hierarchical region cell count data. |
| glassbrain2 | Modified glassbrain function |
| im_sort | A function to sort image paths for large imaging datasets |
| interpolate | Interpolate all AP and z numbers for atlas plates in a whole... |
| isolate_dataset | Selectively isolate forward-warped cells *(W)*. |
| platereturn | Helper background functions |
| pull_atlas | Pull up atlas plate in graphics device. |
| regi_loop | Automatically loops through the image registration process |
| registration2 | Console user interface built on top of 'registration()'... |
| seg_loop | Loop through and segment images in the segmentation channel |
| setup_pl | User friendly way to setup whole brain pipeline analysis |
| SMART | SMART (Semi-manual alignment to reference template): a... |
| voxelize | Generate voxel-based heatmaps |
| voxel_stats | Run statistical tests on voxel-based heatmaps |
