Metadata-Version: 2.1
Name: nd2-extractor
Version: 0.1.0
Summary: A simple tool to extract ND2 files to Zarr, PNG, or TIFF
Home-page: https://github.com/georgeoshardo/nd2_extractor
Author: Georgeos Hardo
Author-email: gh464@cam.ac.uk
Description-Content-Type: text/markdown
Requires-Dist: pims
Requires-Dist: tabulate
Requires-Dist: pims-nd2
Requires-Dist: opencv-python
Requires-Dist: cowpy
Requires-Dist: celluloid
Requires-Dist: termcolor
Requires-Dist: tqdm
Requires-Dist: joblib
Requires-Dist: ipywidgets
Requires-Dist: tifffile
Requires-Dist: pandas
Requires-Dist: pyyaml
Requires-Dist: zarr

# Setup

`pip install nd2-extractor`

For notebook use:

`jupyter nbextension enable --py widgetsnbextension`

# Usage

### From a notebook:

Then launch `nd2_extractor_interactive.ipynb` in a Jupyter notebook.

### From the command line

```
$ nd2_extractor --help
usage: nd2_extractor.py [-h] --ND2_directory ND2_DIRECTORY --save_directory SAVE_DIRECTORY --save_type SAVE_TYPE [--workers WORKERS] [--t_stop T_STOP] [--fill_empty]

Extract and ND2 file to TIFF or PNG (zarr coming soon).

optional arguments:
  -h, --help            show this help message and exit
  --ND2_directory ND2_DIRECTORY
                        The absolute directory of the ND2 file.
  --save_directory SAVE_DIRECTORY
                        The absolute directory of the extraction folder.
  --save_type SAVE_TYPE
                        The file type to save as (PNG/TIFF/zarr).
  --workers WORKERS     The number of joblib workers to send to the extractor.
  --t_stop T_STOP       Extract up until this timepoint.
  --fill_empty          If supplied, will fill empty frames with empty images, or skip saving them. Will be ignored if zarr chosen.
  ```
