View on GitHub


Kinetic Re-Epithelialization Analysis Pipeline

Plate Zip and Index file

The plate zip and index file are the inputs needed to run KREAP.

Plate ZIP

Create a folder with every well you want to be included in your analysis:
file formats zip 1

Create a new zip of these folders:
file formats zip 2

The newly created zip is one of the two inputs for KREAP:
file formats zip 3


The index file has the following structure:

Column Name Description
treatment The treatment group
location Location of the well (relative in the zip)
file_regex A regular expression that helps ignore other (irrelevant) files in a well
time_regex A regular expression that selects the time point of an image
pixel_block_size The pixel block size parameter for Cellprofiler
object_size_min The minimum object size (in pixels)
object_size_max The maximum object size (in pixels)
time_interval The time (in minutes) between images
rotate The images will be rotated (clockwise) by this many degrees (optional)

Here is the index file associated with the zip created in the previous section:
file formats index

The index file doesn’t have to be created in Excel, but it’s convenient.
Any other program that can output tabular files should also work (including any regular text editors).


It’s possible to create zip and index file that contain multiple plates by using extra directories in the zip and index file:
file formats index note


We have prepared a plate zip and index files that can directly be used with KREAP or can be used as a template for your own data:
Sample Zip
Hoechst Plate Index
CellTracker Plate Index

Analyse your data with KREAP

Uploading file to Galaxy KREAP
Run KREAP Image Analysis
Run KREAP Data Modeling
Handling errors in the modeling result