### Run Gradle Eclipse Task Source: https://github.com/glencoesoftware/bioformats2raw/blob/master/README.md Generate Eclipse project files using the Gradle Eclipse task. This is part of the setup for developing in Eclipse. ```bash ./gradlew eclipse ``` -------------------------------- ### Run Basic Conversion Source: https://github.com/glencoesoftware/bioformats2raw/blob/master/README.md Execute the bioformats2raw converter to transform an image file into a Zarr pyramid. Specify the input image file and the output Zarr directory. ```bash bioformats2raw /path/to/file.mrxs /path/to/zarr-pyramid ``` -------------------------------- ### Clone the Repository Source: https://github.com/glencoesoftware/bioformats2raw/blob/master/README.md Clone the bioformats2raw project from GitHub to set up a development environment. This is the first step for building the project locally. ```bash git clone https://github.com/glencoesoftware/bioformats2raw.git ``` -------------------------------- ### Configure External Logback Configuration Source: https://github.com/glencoesoftware/bioformats2raw/blob/master/README.md Specify an external logback configuration file using the JAVA_OPTS environment variable. This allows for custom logging configurations. ```bash JAVA_OPTS="-Dlogback.configurationFile=/path/to/external/logback.xml" \ bioformats2raw ... ``` -------------------------------- ### Run Gradle Build Task Source: https://github.com/glencoesoftware/bioformats2raw/blob/master/README.md Execute Gradle tasks for building the bioformats2raw project. Use './gradlew tasks' to list all available tasks. ```bash ./gradlew tasks ``` -------------------------------- ### Set Zlib Compression Level Source: https://github.com/glencoesoftware/bioformats2raw/blob/master/README.md Configure the compression level for zlib compression, with 0 for no compression and 9 for maximum compression. ```bash bioformats2raw /path/to/file.mrxs /path/to/zarr-pyramid --compression zlib --compression-properties level=9 ``` -------------------------------- ### Set Alternate Temporary Directory and JNA Library Path Source: https://github.com/glencoesoftware/bioformats2raw/blob/master/README.md Configure Java options to specify an alternate temporary directory and the path to the JNA library. This is useful when the default temporary directory is mounted with noexec permissions. ```bash JAVA_OPTS="-Djava.io.tmpdir/path/to/alternate/tmp -Djna.library.path=/path/to/blosc" ``` -------------------------------- ### Include Specific Experimental Reader Source: https://github.com/glencoesoftware/bioformats2raw/blob/master/README.md Use the --extra-readers option to include only a specific experimental reader, such as the MiraxReader. ```bash # only include the reader for .mrxs bioformats2raw /path/to/file.tiff /path/to/zarr-pyramid --extra-readers com.glencoesoftware.bioformats2raw.MiraxReader ``` -------------------------------- ### Configure Reader-Specific Options Source: https://github.com/glencoesoftware/bioformats2raw/blob/master/README.md Pass reader-specific options using the --options flag. Note that the memo file may need to be removed for changes to take effect. ```bash bioformats2raw /path/to/file.mrxs /path/to/zarr-pyramid --options mirax.use_metadata_dimensions=false ``` -------------------------------- ### Specify Exact Number of Resolution Levels Source: https://github.com/glencoesoftware/bioformats2raw/blob/master/README.md Use the --resolutions option to define the precise number of resolution levels in the output pyramid. ```bash bioformats2raw /path/to/file.mrxs /path/to/zarr-pyramid --resolutions 6 bioformats2raw /path/to/file.svs /path/to/zarr-pyramid --resolutions 6 ``` -------------------------------- ### Enable Debug Logging and Redirect Output Source: https://github.com/glencoesoftware/bioformats2raw/blob/master/README.md Run bioformats2raw with the --debug flag to enable verbose logging and redirect standard output to a file. This is helpful for troubleshooting. ```bash bioformats2raw /path/to/file.mrxs /path/to/zarr-pyramid --debug > bf2raw.log ``` -------------------------------- ### Set Blosc Compression Properties Source: https://github.com/glencoesoftware/bioformats2raw/blob/master/README.md Configure Blosc compression with specific codec, level, blocksize, and shuffle type. ```bash bioformats2raw /path/to/file.mrxs /path/to/zarr-pyramid --compression blosc --compression-properties cname=zstd clevel=9 blocksize=0 shuffle=bitshuffle ``` -------------------------------- ### Configure Smallest Resolution Size Source: https://github.com/glencoesoftware/bioformats2raw/blob/master/README.md Set the maximum size for the smallest resolution in the pyramid. Useful for controlling memory usage and file size. ```bash bioformats2raw /path/to/file.mrxs /path/to/zarr-pyramid --target-min-size 128 bioformats2raw /path/to/file.svs /path/to/zarr-pyramid --target-min-size 128 ``` -------------------------------- ### License Information Source: https://github.com/glencoesoftware/bioformats2raw/blob/master/README.md The bioformats2raw converter is distributed under the terms of the GPL license. Refer to LICENSE.txt for detailed information. ```text The converter is distributed under the terms of the GPL license. Please see `LICENSE.txt` for further details. ``` -------------------------------- ### Convert SVS Image File Source: https://github.com/glencoesoftware/bioformats2raw/blob/master/README.md Convert a .svs image file to a Zarr pyramid. This demonstrates the usage with a different supported image format. ```bash bioformats2raw /path/to/file.svs /path/to/zarr-pyramid ``` -------------------------------- ### Set Zstd Compression Level Source: https://github.com/glencoesoftware/bioformats2raw/blob/master/README.md Configure the compression level for zstd compression, with 0 for no compression and 9 for maximum compression. ```bash bioformats2raw /path/to/file.mrxs /path/to/zarr-pyramid --compression zstd --compression-properties level=9 ``` -------------------------------- ### Set Gzip Compression Level Source: https://github.com/glencoesoftware/bioformats2raw/blob/master/README.md Specify the compression level for gzip compression, ranging from 0 (no compression) to 9 (most compression). ```bash bioformats2raw /path/to/file.mrxs /path/to/zarr-pyramid --compression gzip --compression-properties level=9 ``` -------------------------------- ### Set Log Level to TRACE for Verbose Logging Source: https://github.com/glencoesoftware/bioformats2raw/blob/master/README.md Use the --log-level option with TRACE to enable the most verbose logging. This provides detailed information for debugging. ```bash bioformats2raw /path/to/file.mrxs /path/to/zarr-pyramid --log-level TRACE ``` -------------------------------- ### Convert Specific Series from Multi-Series Input Source: https://github.com/glencoesoftware/bioformats2raw/blob/master/README.md Select a subset of series from a multi-series input file using a comma-separated list of indexes. ```bash bioformats2raw /path/to/file.scn /path/to/zarr-pyramid --series 0,2,3,4 ``` -------------------------------- ### ND2 Plate Reader File Naming Convention (Regex) Source: https://github.com/glencoesoftware/bioformats2raw/blob/master/README.md Regular expression for naming ND2 files to be grouped into a single HCS plate. All files for a plate must reside in the same directory and share the same plate name prefix. ```regex (.*_?)Well([A-Z])(\d{2})_Channel(.*)_Seq(\d{4}).nd2 ``` -------------------------------- ### Exclude All Additional Readers Source: https://github.com/glencoesoftware/bioformats2raw/blob/master/README.md Use an empty --extra-readers argument to disable all additional readers and rely solely on Bio-Formats' default readers. ```bash # don't add any additional readers, just use the ones provided by Bio-Formats bioformats2raw /path/to/file.mrxs /path/to/zarr-pyramid --extra-readers ``` -------------------------------- ### TIFF File Naming Convention (Regex) Source: https://github.com/glencoesoftware/bioformats2raw/blob/master/README.md Regular expression for naming TIFF files to be parsed by bioformats2raw. Ensure filenames match this pattern for proper well, field, and channel extraction. ```regex ([A-Z]{1,2})(\d{1,2})_(-?\d+)_(\d+)_(\d+)_([A-Za-z0-9 ,\[\]]+)_(\d+).tif[f]? ``` ```regex ([A-Z]{1,2})(\d{1,2})_(-?\d+)(Z(\d+))?_([A-Za-z0-9 ,\[\]]+)_(\d+)_(\d+)_(\d+)?.tif[f]? ``` ```regex ([A-Z]{1,2})(\d{1,2})_(-?\d+)_.+\[(.+)_([A-Za-z0-9 ,\[\]]+)\]_(\d+)_(\d+)_([0-9-]+)?.tif[f]? ``` === COMPLETE CONTENT === This response contains all available snippets from this library. No additional content exists. Do not make further requests.