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bioformats_jar\n\n[![License](https://img.shields.io/pypi/l/bioformats_jar.svg?color=green)](https://github.com/tlambert03/bioformats_jar/raw/master/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/bioformats_jar.svg?color=green)](https://pypi.org/project/bioformats_jar)\n[![Python Version](https://img.shields.io/pypi/pyversions/bioformats_jar.svg?color=green)](https://python.org)\n[![CI](https://github.com/tlambert03/bioformats_jar/actions/workflows/ci.yml/badge.svg)](https://github.com/tlambert03/bioformats_jar/actions/workflows/ci.yml)\n\n## deprecated\n\nThis package is deprecated.  You should use [scyjava](https://github.com/scijava/scyjava) to download and import jars.  The functionality in this\npackage can be accomplished using scyjava as follows:\n\n```python\nimport jpype\nimport scyjava\n\nscyjava.config.endpoints.append('ome:formats-gpl:6.7.0')\nscyjava.start_jvm()\nloci = jpype.JPackage(\"loci\")\nloci.common.DebugTools.setRootLevel(\"ERROR\")\n```\n\nThis package remains only for packages that already depend on it.\n\n## usage\n\n```python\nfrom bioformats_jar import get_loci, set_loci_log_level\n\n# start the JVM and get the loci module\nloci = get_loci()\n\n# optionally:\nset_loci_log_level(\"DEBUG\")  # by default \"ERROR\"\n```\n\nThe following environment variables can also be used:\n\n- `BIOFORMATS_VERSION` - version of bioformats to use.  by default \"LATEST\"\n- `BIOFORMATS_LOG_LEVEL` - logging level for loci tools. by default \"ERROR\"\n- `BIOFORMATS_LICENSE` - license version of bioformats to use.  must be either\n  `\"gpl\"` or `\"bsd\"`.  By default `\"gpl\"`\n\n*see also:*\n\n- [Bioformats Docs](https://docs.openmicroscopy.org/bio-formats/latest)\n- [Javadocs](https://downloads.openmicroscopy.org/bio-formats/latest/api/) with the loci API\n\n## install\n\n```sh\npip install bioformats-jar\n```\n\n```sh\nconda install -c conda-forge bioformats-jar\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftlambert03%2Fbioformats_jar","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftlambert03%2Fbioformats_jar","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftlambert03%2Fbioformats_jar/lists"}