Platometer is a simple image-processing tool for quantifying colony sizes from arrayed growth experiments in yeast or bacteria. Typical applications include phenotypic screens of mutant collections and synthetic genetic array (SGA) experiments.
WARNING. This package was developed for a set of special applications and may not be applicable to every use case. Please use caution.
Platometer requires Python 3 and a set of packages listed in requirements.txt. We recommend setting up a virtual environment and installing all the required packages via pip:
cd platometer/
virtualenv -p python3.6 platometer_env
source platometer_env/bin/activate
pip install -r requirements.txt
After the installation is complete, it is useful to run a "hello world" Platometer analysis using the Jupyter notebook at examples/Usage_examples.ipynb.
To do so, from within the platometer_env environment install a new ipython kernel:
ipython kernel install --user --name=platometer
Then start jupyter, open examples/Usage_examples.ipynb and select the platometer_env kernel.
jupyter-notebook
For command line useage see platometer.py. Platometer takes four arguments:
python [--plate_format plate_format ] [--chunk_size chunk_size] [--nr_processes nr_processes] path_to_image_folder_list
-
positional arguments:
- path_to_image_folder_list: Path to the file containing the list of folders with images to process (one folder per line, full path; see
examples/folders_to_process.txt)
- path_to_image_folder_list: Path to the file containing the list of folders with images to process (one folder per line, full path; see
-
optional arguments:
- --plate_format: Expected plate format (default=32 48)
- --chunk_size: Number of images per chunk (default=100)
- --nr_processes: Number of cores to use (default: all available)
When ready, run an example case:
python platometer.py examples/folders_to_process.txt
For each processed folder containing images, Platometer generates 2 files:
- jpg_map.txt: contains the list of processed files and their paths
| Column name | Description |
|---|---|
| path | Paths of the images |
| file_id | File IDs |
- all_data.txt: contains the processed data, i.e. colony size quantification for each colony (row, column) position on the plate.
| Column name | Description |
|---|---|
| file_id | File IDs |
| label | Colony IDs |
| col | Column #s of colonies |
| row | Row #s of colonies |
| size | Sizes of colonies |
| col_pxl | Horizontal (x) pixel positions of colonies |
| row_pxl | Vertical (y) pixel positions of colonies |
These files will be placed in an output directory called platometer_$DATE (e.g. platometer_20201012). For more information, including sample images, see examples/Usage_examples.ipynb.
Please direct all questions/comments to Anastasia Baryshnikova ([email protected]).
The main repository for this code is at https://github.com/baryshnikova-lab/platometer. Please subscribe to the repository to receive live updates about new code releases and bug reports.