multifocal-stitching 0.1.1

Algorithms and tools for stitching microscopy images taken at different focal lengths

Multifocal Image Stitching

Documentation	Build Status

Installation

To install from pypi:

pip install multifocal-stitching

Usage

Ensure the images to be stitched are sequentially named in dir.

python -m multifocal_stitching -h
usage: __main__.py [-h] [-v] [-s STITCHING_RESULT] [-d RESULT_DIR] [-r] [--ext EXT] [--no_merge]
                   [--workers WORKERS] [--min_overlap MIN_OVERLAP]
                   [--early_term_thresh EARLY_TERM_THRESH] [--use_wins USE_WINS [USE_WINS ...]]
                   [--peak_cutoff_std PEAK_CUTOFF_STD] [--peaks_dist_threshold PEAKS_DIST_THRESHOLD]
                   [--filter_radius FILTER_RADIUS [FILTER_RADIUS ...]]
                   dir

positional arguments:
  dir                   Base directory

options:
  -h, --help            show this help message and exit
  -v, --verbose         Increase output verbosity (default: False)
  -s STITCHING_RESULT, --stitching_result STITCHING_RESULT
                        Stitching result csv file (default: stitching_result.csv)
  -d RESULT_DIR, --result_dir RESULT_DIR
                        Directory to save merged files (default: merged)
  -r, --exclude_reverse
                        Whether to additionally include img2 on top of img1 (default: False)
  --ext EXT             Filename extension of images (default: .jpg)
  --no_merge            Disable generating merged images (default: False)
  --workers WORKERS     Number of CPU threads to use in FFT (default: 2)
  --min_overlap MIN_OVERLAP
                        Set lower limit for overlapping region as a fraction of total image area
                        (default: 0.125)
  --early_term_thresh EARLY_TERM_THRESH
                        Stop searching when correlation is above this value (default: 0.7)
  --use_wins USE_WINS [USE_WINS ...]
                        Whether to try using Hanning window (default: (0,))
  --peak_cutoff_std PEAK_CUTOFF_STD
                        Number of standard deviations below max value to use for peak finding
                        (default: 1)
  --peaks_dist_threshold PEAKS_DIST_THRESHOLD
                        Distance to consider as part of same cluster when finding peak centroid
                        (default: 25)
  --filter_radius FILTER_RADIUS [FILTER_RADIUS ...]
                        Low-pass filter radii to try, smaller matches coarser/out-of-focus features
                        (default: (100, 50, 20))

Examples