tidyProject: tidyProject

In AndersenLab/easyXpress: A Package to Read, Process, and Analyze Worm Data Generated from CellProfiler’s WormToolbox

tidyProject

Description

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.

AndersenLab/easyXpress documentation built on Dec. 6, 2024, 4:04 a.m.