{"name":"napari-mclabel","display_name":"napari-mclabel","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-mclabel.McLabel","title":"McLabel","python_name":"napari_mclabel.mclabel:McLabel","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-mclabel.McLabel","display_name":"McLabel","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-mclabel","version":"1.0.1.dev0","dynamic":null,"platform":null,"supported_platform":null,"summary":"Napari plugin for semi-automatic labeling of macrophages","description":"# Napari McLabel\n\n## What is the purpose of this tool?\n\nMcLabel is a semi-automatic local thresholding tool that can help to label cellular objects such as macrophages in fluorescence microscopy images. In cases where a global threshold does not yield satisfactory results, a local threshold based on a ROI drawn by the user may give better results. See the video for an example:\n![Mclabel](./img/Mclabel.gif)\n\n\n\n## Installation\n\nThe plugin can be installed using pip:\n```bash\npip install napari-mclabel\n```\n\nAfter succesfull installation the plugin will appear in the plugins menu of napari.\n\n## Usage\n\n![gui](./img/gui.png)\n\nThe GUI of McLabel lives in the right pane of napari. If multiple layers are loaded, select the layer that you want to segment. The theshold finding algorithm is by default is triangle, however there are plenty of alternatives and depending on the data another algorithm might be better suited. \n\n1. Press \"Draw Label\"\n2. Draw a rough outline around the object of interest. \n3. Press \"Compute Label\"\n4. If not satisfied with result, adjust threshold using the slider\n5. Continue with next object\n\n![gui](./img/gui.gif) \n\n## Reference\n\nIf you use McLabel in your work, consider citing our background paper:\nhttps://doi.org/10.1007/978-3-658-41657-7_20\n\n\n\n```tex\n@InProceedings{10.1007/978-3-658-41657-7_20,\nauthor=\"Utz, Jonas\nand Schlereth, Maja\nand Qiu, Jingna\nand Thies, Mareike\nand Wagner, Fabian\nand Brahim, Oumaima B.\nand Gu, Mingxuan\nand Uderhardt, Stefan\nand Breininger, Katharina\",\neditor=\"Deserno, Thomas M.\nand Handels, Heinz\nand Maier, Andreas\nand Maier-Hein, Klaus\nand Palm, Christoph\nand Tolxdorff, Thomas\",\ntitle=\"McLabel\",\nbooktitle=\"Bildverarbeitung f{\\\"u}r die Medizin 2023\",\nyear=\"2023\",\npublisher=\"Springer Fachmedien Wiesbaden\",\naddress=\"Wiesbaden\",\npages=\"82--87\",\nabstract=\"In this work, we present a semi-automatic labelling tool for the annotation of complex cellular structures such as macrophages in fluorescence microscopy images. We present McLabel, a napari plugin that allows users to label structures of interest by simply scribbling outlines around the area of interest, using the triangle thresholding method with post-processing to identify the desired structure. Additionally, manual adaption of the threshold allows for quick and fine-grained local correction of the segmentation. The tool is evaluated in a user study with five experts, who annotated images both with and without the tool. The results show that variability in annotations between experts is reduced when the labelling tool is used and annotation time is reduced by a factor of five on average.\",\nisbn=\"978-3-658-41657-7\"\n}\n```\n\n","description_content_type":"text/markdown","keywords":null,"home_page":"https://gitlab.cs.fau.de/xo04syge/mclabel","download_url":null,"author":"Jonas Utz","author_email":"jonas.utz@fau.de","maintainer":null,"maintainer_email":null,"license":"BSD-3-Clause","classifier":["Development Status :: 2 - Pre-Alpha","Framework :: napari","Topic :: Software Development :: Testing","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3.8","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10","Operating System :: OS Independent","License :: OSI Approved :: BSD License"],"requires_dist":["napari[all]","napari-plugin-engine (>=0.1.4)","imaris-ims-file-reader (>=0.1.5)","numpy","h5py","dask","napari-imaris-loader","scikit-image","scipy"],"requires_python":">=3.8","requires_external":null,"project_url":["Bug Tracker, https://gitlab.cs.fau.de/xo04syge/mclabel/-/issues","Documentation, https://gitlab.cs.fau.de/xo04syge/mclabel/-/blob/main/README.md","Source Code, https://gitlab.cs.fau.de/xo04syge/mclabel","User Support, https://gitlab.cs.fau.de/xo04syge/mclabel/-/issues"],"provides_extra":null,"provides_dist":null,"obsoletes_dist":null},"npe1_shim":true}