Usage

Installation

To use Cenfind, install it from pip. You will have access to subprogram via the command line cenfind <subprogram>.

(.venv) % pip install cenfind

Basic usage

cenfind assumes a fixed folder structure. Specifically, it expects the max-projection to be under the projections folder. Each file in projections is a z-max projected field of view (referred to as field, in the following) containing 4 channels (0, 1, 2, 3). The channel 0 usually contains the nuclei and the channels 1–3 contain centriolar markers.

  1. Run score and indicate the path to the dataset directory, the path to the model (https://figshare.com/articles/software/Cenfind_model_weights/21724421) followed by the index of the nuclei channel (-n) and the channels to score (-c).

In the following example

cenfind score /path/to/dataset /path/to/model/ -n 0 -c 1 2 3

You can run cenfind score only on CPU using the flag –cpu. The option –vicinity controls the radius in pixel around the nuclei under which centrioles are assigned to.

  1. Check that the predictions are satisfactory by looking at the folders visualisations/ and statistics/

Added in version 0.13.0: The outputs can be linked together depending on the applications. Detailed explanation are there Prediction.

Summary statistics

Besides the raw inference data (centriole position and intensity information, nuclei contours and geometry information), the statistics folder contains tabulated data about the distribution of centriole number (statistics.tsv), TSV files for pairs of assigned centrioles and their nucleus if possible. If the cilia are analysed, a TSV file containing the fraction of ciliated cells is saved as well. You can read more about statistics here Statistics.

Running cenfind score in the background

When you exit the shell, running process receive the signal SIGHUP, which aborts them. This is undesirable if you need to close your shell for some reason. Fortunately, you can make your program ignore this signal by prepending the program with the nohup command. Moreover, if you want to run your program in the background, you can append the ampersand &. In practice, run nohup cenfind score ... & instead of cenfind score ....

The output will be written to the file nohup.out and you can peek the progress by running tail -F nohup.out, the flag -F will refresh the screen as the file is being written. Enter Ctrl-C to exit the tail program.

If you want to kill the program cenfind score, run jobs and then kill <jobid>. If you see no jobs, check the log nohup.out; it can be done or the program may have crashed, and you can check the error there.