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CHANGELOG.md

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Changelog

v2.0 - 2022-05-12

  • fixed a bug that lead to invalid dimensions for input images with certain aspect ratios
  • ported pipeline code to nextflow dsl2
  • bumped required nextflow version to 22.04.0
  • moved hosting of pretrained models and test data to Azure (thanks @ebirn)
  • added CITATION.cff
  • added version pinning for R 4.1.3
  • dropped r-shinythemes dependency as r-shiny now has bootstrap 5 support
  • updated r-shiny 1.6.0 > 1.7.1
  • updated tensorflow-base 2.4.1 > 2.7.1
  • updated imagemagick dependency 7.0.11_12 > 7.1.0_33
  • updated r-corrplot dependency 0.88 > 0.92
  • updated r-jpeg dependency 0.1_8.1 > 0.1_9

v1.3.1 - 2021-05-14

  • fixed illegible text in Markdown documents when browsing Github in Dark Mode (thanks @greymonroe for pointing this out)
  • added config profile for BioHPC Genomics cluster at LRZ
  • removed unneeded tensorflow-estimator dependency
  • updated tensorflow-base 2.0.0 > 2.4.1
  • updated imagemagick dependency 7.0.10_28 > 7.0.11_12
  • updated shiny dependency 1.5.0 > 1.6.0
  • updated tidyverse dependency 1.3.0 > 1.3.1
  • updated shinythemes dependency 1.1.2 > 1.2.0
  • updated corrplot dependency 0.84 > 0.88
  • changed container base to micromamba for smaller container images and faster builds
  • added CI tests for conda profile on macOS and additional container engines on linux (charliecloud and podman)

v1.3 - 2021-01-11

  • changed container registry from docker.io to quay.io
  • improved image visualization and plot rendering in Shiny app (see #54) thanks @dschneiderch for input
  • updated scikit-image 0.17.2 > 0.18.1
  • updated imagemagick dependency 7.0.10_23 > 7.0.10_28
  • updated shinycssloaders dependency 0.3 > 1.0.0
  • updated slickr dependency 0.4.9 > 0.5.0
  • added publication doi to pipeline manifest
  • changed (back) download links in pipeline to fetch pretrained models from Dropbox instead of Zenodo (#53)
  • added charliecloud profile (needs nextflow >= 20.12.0-edge)
  • fixed plotting of leaf states over time in Shiny app (when appropriate metadata are provided)
  • added config for LRZ coolmuc2

v1.2.1 - 2020-07-23

  • updated pipeline to fetch trained models from the deposited Zenodo record instead of Dropbox
  • fixed an issue where the DPP addon produced sub-par segmentation results compared to the tools implementation in Deep Plant Phenomics.
  • updated shiny app to show visualizations sorted by filename

v1.2 - 2020-07-15

  • updated shiny dependency 1.4.0 > 1.5.0
  • added a more informative log message if pipeline fails on systems with insufficient memory
  • added --ignore_label parameter to exclude a segmentation class for trait calculation.
  • added --label_spec parameter to allow for mapping of segmentation classes to pixel values of user-supplied segmentation masks. This is a requirement for the --masks parameter now.
  • updated base.config to avoid out-of-memory issues when running with --multiscale
  • added Dockerfile + Conda environment for DPP v2.1.0
  • factored out Shiny dependencies into separate container (should be easier to deploy as a hosted Shiny app now)
  • added --model 'DPP' and --dpp_checkpoint to allow for custom segmentation models, trained using the Deep Plant Phenomics framework
  • added --masks parameter to skip semantic segmentation and run trait extraction using user-supplied masks
  • fixed an issue where the pipeline would crash if the input image contains an alpha channel
  • updated configuration for CBE cluster
  • added log message to show current parameter settings when starting a pipeline run
  • updated scikit-image 0.16.2 > 0.17.2
  • updated imagemagick dependency 7.0.9_27 > 7.0.10_23

v1.1 - 2020-05-13

  • disabled task error strategy for pipeline runs on local computers
  • fixed an issue where the network address of the shiny application was not correctly displayed on computers running MacOS

v1.0 - 2020-04-02

Initial pipeline release