dnasight 1.6.5__tar.gz

dnasight-1.6.5/LICENSE

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+MIT License
+
+Copyright (c) 2025 emilywinther
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

dnasight-1.6.5/PKG-INFO

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+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.
+

dnasight-1.6.5/README.md

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+# 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.
+