Excited Squid Patch

Fixed

• PR#57 - Fix input declaration of the model file for the module: numorph3dunet to be reused for all inputs.
• Remove conda batch from readme, the pipeline does not support conda.
• PR#66 - Set matlab cache directory in numorph_stitch to fix concurrency issues when running multiple samples.

1.0.0 - Excited Squid

Initial release of nf-core/lsmquant, created with the nf-core template.

nf-core/lsmquant is a bioinformatics pipeline that performs preprocessing and analysis of light-sheet microscopy images of tissue-cleared samples. The pipeline consists of 3 major components: Preprocessing to reconstruct the 3D image from raw light-sheet data, Cell-Nuclei quantification, and Registration to the Allen Brain Reference Atlas.

The pipeline is mainly based on the NuMorph (Nuclear-Based Morphometry) toolbox and originally written by @CaroAMN.

Thank you to everyone who has contributed to the initial release: @mashehu, @luiskuhn, @famosab, @tatianawoller, @irelamb, @bpavie, @mapo9, @SusiJo, @d4straub