spotiflow
Accurate and efficient spot detection for microscopy data
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Download Latest Version (.zip)- bug_report.md
- feature_request.md
- cibuildwheel.yml
- docker-publish.yml
- docs.yaml
- CODEOWNERS
- PULL_REQUEST_TEMPLATE.md
- logo_squared.png
- overview.png
- spotiflow_logo.png
- spotiflow_transp_small.png
- spotiflow_logo.png
- spotiflow_napari_gui.png
- spotiflow_napari_preds.png
- api.rst
- cli.rst
- conf.py
- finetune.rst
- index.rst
- installation.rst
- napari.rst
- pretrained.rst
- train.rst
- make.bat
- Makefile
- 1_train.ipynb
- 2_inference.ipynb
- 3_finetune.ipynb
- 4_train_3d.ipynb
- analyze_spot_clusters.py
- annotation_ui.py
- run_starfish_spotiflow.py
- predict_3d.py
- predict_zarr_multigpu.py
- train_simple.py
- train_simple_3d.py
- __init__.py
- pipeline.py
- test_crop.py
- test_fliprot.py
- test_intensity_shift.py
- test_noise.py
- test_rotation.py
- test_scale.py
- test_translation.py
- test_pipeline.py
- __init__.py
- base.py
- crop.py
- fliprot.py
- intensity_shift.py
- noise.py
- rotation.py
- scale.py
- translation.py
- utils.py
- __init__.py
- crop.py
- fliprot.py
- intensity_shift.py
- noise.py
- rotation.py
- translation.py
- __init__.py
- __init__.py
- check.py
- predict.py
- train.py
- test_datasets.py
- __init__.py
- spots.py
- spots3d.py
- LICENSE.txt
- nanoflann.hpp
- filters.cpp
- filters3d.cpp
- point_nms.cpp
- point_nms3d.cpp
- spotflow2d.cpp
- spotflow3d.cpp
- __init__.py
- resnet.py
- unet.py
- __init__.py
- adaptive_wing.py
- __init__.py
- bg_remover.py
- config.py
- post.py
- pretrained.py
- spotiflow.py
- trainer.py
- img_hybiss_2d.tif
- img_synth_3d.tif
- img_terra_2d.tif
- timelapse_telomeres_2d.tif
- __init__.py
- datasets.py
- __init__.py
- spotiflow_wrapper.py
- test_model_saveload.py
- test_prediction.py
- __init__.py
- ci.py
- fitting.py
- get_file.py
- matching.py
- parallel.py
- peaks.py
- utils.py
- __init__.py
- test_data.py
- test_fit.py
- test_model.py
- test_peaks.py
- test_training.py
- test_training_simple.py
- utils.py
- .gitignore
- .pre-commit-config.yaml
- CITATION.cff
- docker-env-config.yml
- Dockerfile
- LICENSE
- MANIFEST.in
- pyproject.toml
- README.md
- setup.cfg
- setup.py
- tox.ini
# Installation Guide
git clone https://github.com/weigertlab/spotiflow
Downloads the entire project code from GitHub to your computer.
cd spotiflow
Moves into the project folder you just downloaded.
2. Official Install Script
Easy Recommended- Python 3 Python is required to use pip.
pip install torch
Installs the package published on PyPI directly β no need to clone the source.
pip install spotiflow
Installs the package published on PyPI directly β no need to clone the source.
Pulled directly from this repo's README.
3. Docker
Easy- Git Needed to download the project code from GitHub.
- Docker Desktop Needed to build and run containers. Install it and keep it running in the background.
Note that the current implementation of Spotiflow in Docker only supports CPU inference.
Type this command into your terminal and run it.
Pulled directly from this repo's README.
4. Python
Easypip install torch
Installs the package published on PyPI directly β no need to clone the source.
pip install spotiflow
Installs the package published on PyPI directly β no need to clone the source.
pip install -e ".[testing]"
Installs the Python libraries listed in requirements.txt (or similar).
pip install -e ".[docs]"
Installs the Python libraries listed in requirements.txt (or similar).
Pulled directly from this repo's README.