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nf-core/lsmquant: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

1.0.1 - Patch Release - 2026-04-29

Fixed

  • PR#57 - Fix input declaration of the model file for the module: numorph3dunet to be reused fo all inputs.
  • remove conda batch from readme, the pipeline does not support conda.

v1.0.0 - Excited Squid

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

Added

The main functionalities of the NuMorph toolbox are added up until the nuclei quantification via a 3DUnet.

local Modules:

  • numorphintensity
  • numorphalign
  • numorphstitch
  • numorphresample
  • numorphregister
  • numorph3dunet
  • mat2json
  • stagefiles

nf-core Modules:

  • multiqc
  • unzip

local subworkflows:

  • numorphpreprocessing:
    • numorphintensity
    • numorphalign
    • numorphstitch
    • mat2json
  • ara-registration
    • numorphresample
    • numorphregister
    • mat2json

Fixed

Dependencies

Custom numorph container numorphpreprocessing, numorphanalyze, mat2json, and numorph3dunetare on the nf-core quay io repository. Compiled matlab application numorph_preprocessing, mat2json and the source code for the 3Dunet python package are public repositories. The source code of the tools are found here NuMorph_dev

Deprecated