Live-dead

Image processing script for calculation of cell viability of 3D spheroids in microfluidic arrays.

• Installation
• Image pre-processing
• Running the script
  • Absolute cell viability
  • Relative cell viability
• Configuration
  • Default settings

Installation

pip install -r requirements.txt

Image pre-processing

The best performance is assumed for the images of single quadruplet device. For calculation of cell viability two channels (0:live and 1:dead) are required.

Running the script

python live-dead.py

Absolute cell viability

Estimation of the absolute cell viability values for single time point:

1. Analysis of images
2. Browse - Select the folder with the example file
3. Select the image
4. Load image
5. Grid

6. Report
7. Save the results

Relative cell viability

Estimation of the relative cell viability values between two time points (e.g., before and after drug treatment):

1. Relative cell viability
2. Browse folder with the report *.csv files
3. Load day1 report file
4. Load day3 report file
5. Select which rows of microwells to include into the analysis
6. Report (the values are automatically coppied in the clipboard)

Configuration

The settings included:

• MF arrays with 100, 200 and 300 um microwells;
• MCF-7 and DCBXTO.58 cell types

The number of the rows and wells could be changed

Default settings

settings = {
    'folder' : '/Users/viprorok/Google Диск/Laba/Github/Im_processing/Synergy index/',
    'invert_flag' : True,
    'autocontrast_flag' : True,
    'scaling_factor': {'100 um': 6, '200 um': 12, '300 um': 12},       ### 6 for 100um and 12 for 200 um and 300 um
    'rows' : 4,
    'columns' : 25,
    'radius' : {'100 um': 30, '200 um': 55, '300 um': 85},     ### [30 for 100 um] and [85 for 300um] [55 for 200um]
    'offset' : 10,
    'flag_100' : False,
    'flag_300' : True,
    'flag_200': False,
    'devices' : 1,
    'device_types':['100 um','200 um','300 um'],
    'default_device_type': 2,
    'cell_types': ['MCF-7', 'DCBXTO.58'],
    'default_cell_type': 0,
    'live_range' : {'MCF-7' : [0.015, 0.09], 'DCBXTO.58': [0.012, 0.085]}, ##  [0.015, 0.09] for MCF-7 cells ; [0.012, 0.085] for .58
    'dead_range' : {'MCF-7' : [0.08, 0.02], 'DCBXTO.58': [0.085, 0.02]}, ## [0.08, 0.02] for MCF-7 cells ; [0.085, 0.02] for .58
    'hist_flag' : True,
    'ch_flag' : False,
    'dil_flag': True,
    'cv_threshold': 0.5,
    'synergy_flag': True,
    'cv_flag': False, 
    '3D_text': True,
    '3D_alpha': 0.5,
    'conc_flag': False
    }

The settings could be saved in config.json and loaded if needed.