{"name":"napari-dmc-brainmap","display_name":"dmc_brainmap","visibility":"public","icon":"","categories":[],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-dmc-brainmap.ParamsWidget","title":"Create params.json file","python_name":"napari_dmc_brainmap.params:ParamsWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-dmc-brainmap.StitchingWidget","title":"Stitch tif images","python_name":"napari_dmc_brainmap.stitching:StitchingWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-dmc-brainmap.PaddingWidget","title":"Padding of stitched images to match atlas resolution","python_name":"napari_dmc_brainmap.padding:PaddingWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-dmc-brainmap.PreprocessingWidget","title":"Make widget to perform preprocessing operations","python_name":"napari_dmc_brainmap.preprocessing:PreprocessingWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-dmc-brainmap.RegistrationWidget","title":"Make registration widget to start registration GUI","python_name":"napari_dmc_brainmap.registration:RegistrationWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-dmc-brainmap.SegmentWidget","title":"Make segmentation widget","python_name":"napari_dmc_brainmap.segment:SegmentWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-dmc-brainmap.ResultsWidget","title":"Make widget to create results file","python_name":"napari_dmc_brainmap.results:ResultsWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-dmc-brainmap.VisualizationWidget","title":"Make widget to visualize data","python_name":"napari_dmc_brainmap.visualization:VisualizationWidget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-dmc-brainmap.ParamsWidget","display_name":"Create params file (general info -- ALWAYS start with this!)","autogenerate":false},{"command":"napari-dmc-brainmap.StitchingWidget","display_name":"Stitch tif images","autogenerate":false},{"command":"napari-dmc-brainmap.PaddingWidget","display_name":"Padding of stitched images to match atlas resolution","autogenerate":false},{"command":"napari-dmc-brainmap.PreprocessingWidget","display_name":"Preprocessing","autogenerate":false},{"command":"napari-dmc-brainmap.RegistrationWidget","display_name":"Registration","autogenerate":false},{"command":"napari-dmc-brainmap.SegmentWidget","display_name":"Segmentation","autogenerate":false},{"command":"napari-dmc-brainmap.ResultsWidget","display_name":"Create results file","autogenerate":false},{"command":"napari-dmc-brainmap.VisualizationWidget","display_name":"Visualize data","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"napari-dmc-brainmap","version":"0.1.7b15","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"DMC-BrainMap is an end-to-end tool for multi-feature brain mapping across species","description":"\n# napari-dmc-brainmap\n*DMC-BrainMap is an end-to-end tool for multi-feature brain mapping across species.*  \nThis [napari](https://napari.org/stable/) plugin was generated with [Cookiecutter](https://github.com/cookiecutter/cookiecutter) using napari's [cookiecutter-napari-plugin](https://github.com/napari/cookiecutter-napari-plugin) template.\n\n[![License BSD-3](https://img.shields.io/pypi/l/napari-dmc-brainmap.svg?color=green)](https://github.com/hejDMC/napari-dmc-brainmap/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-dmc-brainmap.svg?color=green)](https://pypi.org/project/napari-dmc-brainmap)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-dmc-brainmap.svg?color=green)](https://python.org)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-dmc-brainmap)](https://napari-hub.org/plugins/napari-dmc-brainmap)\n\n\n## Quick start\nA detailed guide and tutorial can be found on the [Wiki pages of this repo](https://github.com/hejDMC/napari-dmc-brainmap/wiki).\n\n### Installation\n\nDMC-BrainMap is a plugin for [napari](https://napari.org/stable/). Hence, you first need to install napari and subsequently the DMC-BrainMap plugin via the plugin manager. To install napari, we recommend to install napari into a clean virtual environment using *conda* or *venv*. Please refer to the [napari installation guide](https://napari.org/stable/tutorials/fundamentals/installation.html#napari-installation) for more information and [for information on installing napari as a bundled app](https://napari.org/stable/tutorials/fundamentals/installation.html#napari-installation).  \n\n#### Step 1: Setup the virtual environment (Python 3.10)\n\n```\nconda create -y -n napari-env -c conda-forge python=3.10\nconda activate napari-env\n```\n\n#### Step 2: Install napari\n\n```\npython -m pip install \"napari[all]\"\n```\n\n#### Step 3: Install napari-dmc-brainmap\n\nYou can install `napari-dmc-brainmap` via the napari plugin manager or via [pip](https://pypi.org/project/napari-dmc-brainmap/):\n\n    pip install napari-dmc-brainmap\n\n### Usage\n\nPlease refer to the Wiki pages for detailed instructions and a short tutorial on how to use DMC-BrainMap. When working with DMC-BrainMap on your own data, please keep the following points in mind:\n- DMC-BrainMap requires single-channel 16-bit .tif/.tiff images to work (in principle 8-bit also work)\n- DMC-BrainMap requires that your data is organized by animals in separate folders (you can pool data later down the lane)\n- DMC-BrainMap uses 5 channel labels (`dapi`, `green`, `n3`, `cy3`, `cy5`) corresponding to blue, green, orange, red and far red channels. *However, these are only labels, you can assign them as you please. Hence, you can use DMC-BrainMap also for non-fluorescence data given you converted your images to single-channel 16-bit .tif/.tiff images*. Please contact us if you need to use more than 5 channels.\n- It is essential that you structure your data in the following way (hierarchical organization, same name for images in different channels, channel labels are selected by you), **otherwise DMC-BrainMap won't work**:\n```\nanimal_id-001\n│\n└───stitched\n│   │\n│   └───dapi\n│   |    │   animal_id-001_001.tiff\n│   |    │   animal_id-001_002.tiff\n|   │    |   animal_id-001_003.tiff\n│   |    │   animal_id-001_004.tiff\n│   |    │   ...\n│   │   \n│   └───green\n│       │   animal_id-001_001.tiff\n│       │   animal_id-001_002.tiff\n│       │   animal_id-001_003.tiff\n│       │   animal_id-001_004.tiff\n│       │   ...\n│   \nanimal_id-2\n│   ...\n```\n\n## Documentation\nDocumentation on DMC-BrainMap's source code can be found on the project's [Read the Docs page](https://napari-dmc-brainmap.readthedocs.io/en/latest/#).\n\n## Seeking help or contributing\n\nDMC-BrainMap is an open-source project, and we welcome contributions of all kinds. If you have any questions, feedback, or suggestions, please feel free to open an issue on this repository. \n\n## License\n\nDistributed under the terms of the [BSD-3](https://github.com/teamdigitale/licenses/blob/master/BSD-3-Clause) license,\n\"napari-dmc-brainmap\" is free and open source software\n\n## Citing DMC-BrainMap\n\nIf you use DMC-BrainMap in your scientific work, please cite:\n```\nJung, F., Cao, X., Heymans, L., Carlén, M. (2026) \"DMC-BrainMap is an open-source, end-to-end tool for multi-feature brain mapping across species\", Cell Reports Methods, https://doi.org/10.1016/j.crmeth.2026.101302\n```\n\nBibTeX:  \n``` bibtex\n@article{Jung2026a,\ntitle = {DMC-BrainMap is an open-source, end-to-end tool for multi-feature brain mapping in different species},\njournal = {Cell Reports Methods},\nvolume = {6},\nnumber = {2},\npages = {101302},\nyear = {2026},\nissn = {2667-2375},\ndoi = {https://doi.org/10.1016/j.crmeth.2026.101302},\nurl = {https://www.sciencedirect.com/science/article/pii/S2667237526000020},\nauthor = {Felix Jung and Xiao Cao and Loran Heymans and Marie Carlén}\n}\n```\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":"Felix Jung","author_email":"jung.neurosc@gmail.com","maintainer":null,"maintainer_email":null,"license":"BSD-3-Clause","classifier":["Development Status :: 4 - Beta","Framework :: napari","Intended Audience :: Developers","License :: OSI Approved :: BSD License","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3 :: Only","Programming Language :: Python :: 3.10","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["numpy==1.26.4","pandas==2.0.1","matplotlib==3.8.3","seaborn==0.12.2","scikit-learn==1.6.1","scikit-image==0.22.0","scikit-spatial==7.2.0","tifffile==2023.2.28","magicgui==0.8.1","qtpy==2.4.1","opencv-python==4.9.0.80","natsort==8.4.0","imagecodecs==2025.3.30","mergedeep==1.3.4","aicsimageio==4.14.0","aicspylibczi==3.1.2","aicssegmentation==0.5.3","distinctipy==1.3.4","bg_atlasapi==1.0.2","shapely==2.0.1"],"requires_python":"==3.10.*","requires_external":null,"project_url":null,"provides_extra":null,"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}