multifish - 2.6.0

New Features * Added --rsfish_background parameter for controlling RS-FISH background subtraction * Added --rsfish_intensity parameter for controlling RS-FISH intensity calculation * Updated to RS-FISH-Spark 1.0.2

Bug Fixes * Fixed tile tokenization for compatibility with Nextflow 24.x

Full Changelog: https://github.com/JaneliaSciComp/multifish/compare/2.5.0...2.6.0

- Jupyter Notebook
Published by krokicki about 2 years ago

multifish - 2.5.0

New Features

• Added "all" option for stitching_ref
• Made stitching retile step optional
• Added per-channel RS-FISH parameters
• Improved documentation

Bug Fixes

• Removed unnecessary --nv flag to address issues with newer GLIBC systems
• error in intensity_measurements.py by @wangyuhan01 in https://github.com/JaneliaSciComp/multifish/pull/14
• git clone needs --recursive as external-modules/spark is a submodule by @orena1 in https://github.com/JaneliaSciComp/multifish/pull/23

New Contributors

• @wangyuhan01 made their first contribution in https://github.com/JaneliaSciComp/multifish/pull/14
• @orena1 made their first contribution in https://github.com/JaneliaSciComp/multifish/pull/23

Full Changelog: https://github.com/JaneliaSciComp/multifish/compare/2.4.0...2.5.0

- Jupyter Notebook
Published by krokicki over 2 years ago

multifish - 2.4.0

Full Changelog: https://github.com/JaneliaSciComp/multifish/compare/2.3.0...2.4.0

- Jupyter Notebook
Published by krokicki almost 4 years ago

multifish - 2.3.0

• Fixed warp spots when using RS-FISH
• Update default parameters to accommodate large data sets
• Use AWS ECR by default for fetching containers to eliminate throttling errors with DockerHub
• Many documentation improvements

Full Changelog: https://github.com/JaneliaSciComp/multifish/compare/2.2.0...2.3.0

- Jupyter Notebook
Published by krokicki over 4 years ago

multifish - 2.2.0

• Added support for RS-FISH spot detection
• Fixed pipeline so that flatfield correction is used
• Improved directory naming to reduce conflicts on clusters
• Improved error reporting for Spark jobs

Full Changelog: https://github.com/JaneliaSciComp/multifish/compare/2.1.0...2.2.0

- Jupyter Notebook
Published by krokicki over 4 years ago

multifish - Release 2.1.0

Bug fixes and better example data sets, including a "tiny" data set that can be run quickly for regression testing.

- Jupyter Notebook
Published by krokicki over 4 years ago

multifish - Release 2.0.0

Significant refactoring of the parameters to make it easy to run the pipeline on Nextflow Tower. 1) Fixed several issues related to running on AWS 2) Added a download step which downloads a manifest of files, to make it easier to test the demo sets on AWS 3) Greatly simplified directory handling with sharedworkdir 4) Added a publishing step, to copy data onto S3 after the pipeline is complete 5) Added support for CZI file name patterns in the stitching pipeline

- Jupyter Notebook
Published by krokicki over 4 years ago

multifish - Release 1.4.0

Snapshot stable release before merging tower branch for running on Nextflow Tower.

- Jupyter Notebook
Published by krokicki over 4 years ago

multifish - Release 1.1.0

Updated to new version of spot assignment, and made improvements to demo scripts and documentation.

- Jupyter Notebook
Published by krokicki over 5 years ago

multifish - Release 1.0.0

The pipeline is now feature complete and successfully runs end-to-end on medium test data with both local and LSF executors.

- Jupyter Notebook
Published by krokicki over 5 years ago