Man pages for Russel88/RCon3D
Analysis of Confocal Images of Microbial Biofilms
| center_of_mass | Find Center of Mass in images |
| clumps | Find 3D aggregates/clumps |
| clumps_dist | Find distances between 3D aggregates/clumps |
| clumps_plot | Plot 3D aggregates |
| co_agg | 3D co-aggregation |
| create_nulls | Create RDS for all empty pixels |
| create_random | Create random image |
| cross_ratio | 3D cross-ratio |
| extract_layers | Extract layers |
| findIMG | Find arrays created with 'loadIMG' or 'tiff_to_array' |
| layer_split | Split quantification in Top, Middle and Bottom |
| layer_stand | Trim and standardize quantification |
| loadIMG | Load .tif images into R |
| merge_channels | Create RDS for a combination of channels |
| morphIMG | Apply mathematical morphology kernel on image and save as RDS |
| occupancy | 3D Occupancy |
| quant | Quantifies the pixels in images |
| smoothIMG | Median smooth image and save as RDS |
| threshIMG | Apply thresholding on image and save as RDS |
| tiff_to_array | Make Array from .tif file(s) |
| xy_splits | Analyses for each xy position |
