fltower 0.2.0

Software for cytometry analysis.

FLtower

1. Installation

OS	Linux	Windows	Mac
compatibility	Yes	Yes	Yes

[Optional] Install conda

We use conda environment to avoid version problem between FLtower dependencies and other applications.

We recommend to download the lighter version via Miniconda (if you only intend to use FLtower without developing new feature).

[Optional] Create the environment

conda create -n fltower python=3.11
conda activate fltower

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Install FLtower from PyPi

pip install fltower

To check if FLtower is well installed, run:

fltower --help

2. Usage

Folder structure

Your input data folder should look like this:

my_root/
├── my_data/
│   ├── RBS library - 7975 - Caff_Experiment_M9 - 7975 - P1 - Caff_A1.fcs
│   ├── ...
│   ├── RBS library - 7975 - Caff_Experiment_M9 - 7975 - P1 - Caff_H12.fcs
│   └── parameters.json

With 96 FCS files and one parameters.json file.

Parameter file

The parameter file brings together all the plot configurations.

You can find a template here, or just run fltower inside a folder without any parameters.json file and the software will generate for you a parameters_template.json.

Running FLtower (5~10 min)

If you use it, remember to activate your environment (conda activate fltower),

Basic run

You can run FLtower from your data folder (in this example: cd my_root/my_data/) with just this keyword:

fltower

And the software will generate a results_<DATE>_<TIME> folder inside your input folder like this:

my_root/
└── my_data/
    ├── RBS library - 7975 - Caff_Experiment_M9 - 7975 - P1 - Caff_A1.fcs
    ├── ...
    ├── RBS library - 7975 - Caff_Experiment_M9 - 7975 - P1 - Caff_H12.fcs
    ├── parameters.json
    └── results_20241127_094857/
        ├── plots/
        ├── .../
        ├── statistics/
        ├── summary_report.pdf
        └── used_parameters.json

[Optional] Custom run

You can also run FLtower from anywhere by specifying your input data folder, where you want to save outputs and where are located the parameter file:

fltower --input my_root/my_data/ --output my_root/OUTPUT/ --parameters my_root/parameters.json

Or with the shortcuts:

fltower -I my_root/my_data/ -O my_root/OUTPUT/ -P my_root/parameters.json

Then your folder structure should look like this:

my_root/
├── parameters.json
├── my_data/
│   ├── RBS library - 7975 - Caff_Experiment_M9 - 7975 - P1 - Caff_A1.fcs
│   ├── ...
│   └── RBS library - 7975 - Caff_Experiment_M9 - 7975 - P1 - Caff_H12.fcs
└── OUTPUT/
    └── results_20241127_094857/
        ├── plots/
        ├── .../
        ├── statistics/
        ├── summary_report.pdf
        └── used_parameters.json

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Compare 2 FLtower results

fltower_compare -P parameters.json -O /home/Documents/test --exp1_dir Plate_1_6h/ --exp2_dir Plate_1_24h/  --exp1_label 6h --exp2_label 24h

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3. Support

If you encounter any issues or have questions, open an issue in the GitHub repository.