├── .circleci └── config.yml ├── .gitattributes ├── .gitignore ├── .pep8speaks.yml ├── CHANGELOG.md ├── README.md ├── codecov.yml ├── docs ├── Makefile ├── _autosummary │ ├── merlin.analysis.rst │ ├── merlin.core.rst │ ├── merlin.util.rst │ └── merlin.view.rst ├── _modules │ ├── bokeh.rst │ ├── merlin.analysis.rst │ ├── merlin.core.rst │ ├── merlin.rst │ ├── merlin.util.rst │ ├── merlin.view.rst │ ├── merlin.view.widgets.rst │ ├── modules.rst │ └── setup.rst ├── _static │ └── merlin_headline.png ├── api.rst ├── conf.py ├── contributing.rst ├── index.rst ├── installation.rst ├── make.bat ├── modules.rst ├── tasks.rst └── usage.rst ├── license.md ├── merlin ├── __init__.py ├── __main__.py ├── analysis │ ├── __init__.py │ ├── decode.py │ ├── exportbarcodes.py │ ├── filterbarcodes.py │ ├── generatemosaic.py │ ├── globalalign.py │ ├── optimize.py │ ├── partition.py │ ├── plotperformance.py │ ├── preprocess.py │ ├── segment.py │ ├── sequential.py │ ├── slurmreport.py │ ├── testtask.py │ └── warp.py ├── core │ ├── __init__.py │ ├── analysistask.py │ ├── dataset.py │ └── executor.py ├── data │ ├── __init__.py │ ├── codebook.py │ └── dataorganization.py ├── ext │ └── default.mplstyle ├── merlin.py ├── plots │ ├── __init__.py │ ├── _base.py │ ├── decodeplots.py │ ├── filterplots.py │ ├── optimizationplots.py │ ├── segmentationplots.py │ └── testplots.py ├── util │ ├── __init__.py │ ├── aberration.py │ ├── barcodedb.py │ ├── barcodefilters.py │ ├── binary.py │ ├── dataportal.py │ ├── decoding.py │ ├── deconvolve.py │ ├── imagefilters.py │ ├── imagereader.py │ ├── legacy.py │ ├── matlab.py │ ├── registration.py │ ├── simulator.py │ ├── snakewriter.py │ ├── spatialfeature.py │ └── watershed.py └── view │ ├── __init__.py │ ├── __main__.py │ ├── merlinview.py │ └── widgets │ ├── __init__.py │ └── regionview.py ├── requirements.txt ├── setup.py └── test ├── auxiliary_files ├── test.dax ├── test.inf ├── test_0_0.tif ├── test_0_1.tif ├── test_0_2.tif ├── test_0_3.tif ├── test_0_4.tif 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