Metadata-Version: 2.4
Name: dnasight
Version: 1.6.5
Summary: DNAsight
Author-email: Emily Winther Sørensen <es@chem.ku.dk>, "Julius B. Kirkegaard" <juki@di.ku.dk>
License-Expression: GPL-3.0-or-later
Project-URL: Homepage, https://github.com/emilywinther/dnasight
Project-URL: Repository, https://github.com/emilywinther/dnasight
Project-URL: Issues, https://github.com/emilywinther/dnasight/issues
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: roifile
Requires-Dist: scikit-image
Requires-Dist: scipy
Requires-Dist: tifffile
Requires-Dist: numpy
Requires-Dist: opencv-python-headless
Requires-Dist: matplotlib
Requires-Dist: pandas
Requires-Dist: tqdm
Requires-Dist: torch
Requires-Dist: torchvision
Requires-Dist: albumentations
Requires-Dist: imagecodecs
Requires-Dist: scikit-learn
Requires-Dist: numba
Requires-Dist: mahotas
Requires-Dist: dearpygui
Requires-Dist: trackpy
Requires-Dist: pyinstaller
Requires-Dist: certifi
Dynamic: license-file

# DNAsight  
Code for DNA and cluster segmentation

To train a model run e.g.
```
python dnasight-cmd.py train --folder "data_location1/" "data_location2/" --save_dir model/ --save_plots
```

Examples:


GAF:
```
python dnasight-cmd.py run \
    --folder "data/" \
    --output "output/" \
    --unet "model/unet.pt" \
    --cluster \
    --cluster_quantification \
    --pixel_size_csv "pixelsize.csv" \
    --coverage_quantification \
    --dna_calibration "path=dna_callibration_data/,dna_bp=1059,pixel_size_nm=4.0,perc_low=20,perc_high=95,dna_calibration_threshold=0.8" \
    --dna_calibration "path=second_calibration/,dna_bp=482,pixel_size_nm=2.5"
```

IHF / POLYAMINES:
```

```

COHESIN CTCF / SMC PROTEINS:
```

```

NUCLEOSOMES:
```

```

Or run GUI version:

```
python dnasight-gui.py
```

and choose options in the UI.

