AMATERAS

Image analysis for AMATERAS microscope

Setup

git clone https://github.com/FrickTobias/amateras.git
cd amateras
pip install -e .

Update

cd amateras
git pull

Usage

amateras bigcellfinder -h

Examples

Minimal

amateras bigcellfinder tests/img.tif --n-cells 100 > ~/Desktop/positions.txt

Write qc output

amateras bigcellfinder tests/img.tif --n-cells 100 --qc-outdir ~/Desktop/bigcells-qc-output > ~/Desktop/positions.txt

Include details of all steps in analysis

amateras bigcellfinder tests/img.tif --n-cells 100 --qc-outdir ~/Desktop/bigcells-qc-output --details > ~/Desktop/positions.txt

Advanced examples

Try modifying program settings if cells are missing or being falsely identified

Use automatic thresholding

amateras bigcellfinder tests/img.tif --auto-thresh --n-cells 100 > ~/Desktop/positions.txt

Set thresholding manually (corresponds to highest px value for black area of cell lowest px value for white area of cell)

amateras bigcellfinder tests/img.tif --black-thresh 90 --white-thresh 150 --n-cells 100 > ~/Desktop/positions.txt

Filter out high density regions

amateras bigcellfinder tests/img.tif --final-filter --n-cells 100 > ~/Desktop/positions.txt