tidyProject

Tidies up .TIF files exported from imaging platform and makes thumbnails of wells and plates.

Usage

tidyProject(project_dir, rm_other = FALSE, plates = "all", max_dim = 512)

Arguments

project_dir

the full path to the project directory. This folder should contain .TIF images exported from the imaging platform.

rm_other

logical, remove non-TIF files and folders after the .TIF files are moved to raw_images subfolder? Default is FALSE. Set to TRUE if you are certain you want to remove non-TIF files and folders in the project_dir after .TIFs are moved.

plates

a vector with plate numbers to make thumbs for. This vector is used to match plate patterns in the filelist.
"all" will make thumbs for all plates.
13:72 will make thumbs for wells plates p13 - p72.
c(1, 3, 106) will make thumbs for plates p01, p03, and p106.

max_dim

The maximum dimension of the resized images in pixels. The default value is 512, which scales a 2048 pixel image to 6.25 percent of its original resolution.

Value

Folders named raw_images, raw_image_thumbs, and raw_plate_thumbs are created under the directory specified by project_dir. These folders match the directory structure needed to process the images with

AndersenLab/CellProfiler.