cell-analysis-tools 0.0.8

cell analysis tools

CELL ANALYSIS TOOLS

A library for loading, processing and summarizing flim data.

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Dependencies

• numpy
• tifffile
• from pathlib import Path
• read_roi
• os
• matplotlib
• re
• skimage
• pandas as pd

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Installation

To install this library change directory to the root of the cell_analysis_tools folder then execute:

$ pip install -e .

you should then be able to import it into your script

import cell_analysis_tools

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Summarizing your data

The cell_analysis_tools library contains a script main.py that can be used to summarize your data.

The script was created with 30 images from the T cell dataset used in the paper Classification of T-cell activation via autofluorescence lifetime imaging if is strongly recommended you run the code as is with this dataset to makes sure you know how to modify it to your needs.

The algorithm takes in a dictionary of paths pointing to the various tiffs that will be used as data or masks.

set_dict = {
        "sdt": path_sdt,
        "mask_whole_cell" : path_m_cell, # store paths to cell/cyto masks
        "mask_cyto" : path_m_cyto,
        "photons": path_photons,
        "a1" : path_a1,
        "a2" :path_a2,
        "t1" : path_t1,
        "t2" : path_t2,
        "chisq" : path_chisq,
        }