add Zenodo links, references and correspondence to READMEs and update…

… env
Immunodynamics-Engel-Lab · Jul 1, 2024 · f7dbab4 · f7dbab4
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diff --git a/README.md b/README.md
@@ -81,6 +81,14 @@ Each workflow directory contains a **README** with detailed information on
 - where to find **example data** to test the workflow
 
 ## Example data
-Generally all example data to test the workflows can be found on [Zenodo]().
+Generally all example data to test the workflows can be found on [Zenodo](https://doi.org/10.5281/zenodo.11913042).
 
+## Correspondence
+[**Prof. Dr. Daniel R. Engel**](mailto:[email protected]): Department of Immunodynamics, Institute of Experimental Immunology and Imaging, University Hospital Essen, Essen, Germany
 
+http://www.immunodynamics.de
+
+## References
+1. Veselkov, K., Sleeman, J., Claude, E. et al. BASIS: High-performance bioinformatics platform for processing of large-scale mass spectrometry imaging data in chemically augmented histology. Sci Rep 8, 4053 (2018). https://doi.org/10.1038/s41598-018-22499-z
+2. Grélard, F., Legland, D., Fanuel, M. et al. Esmraldi: efficient methods for the fusion of mass spectrometry and magnetic resonance images. BMC Bioinformatics 22, 56 (2021). https://doi.org/10.1186/s12859-020-03954-z
+3. imzy. imzy: A new reader/writer interface to imzML and other imaging mass spectrometry formats. GitHub repository (2022). https://github.com/imzy/imzy
diff --git a/if_segmentation_flow/README.md b/if_segmentation_flow/README.md
@@ -64,4 +64,4 @@ data
 ```
 
 ## Example data
-Example data to run this workflow can be found on [Zenodo]().
+Example data to run this workflow can be found on [Zenodo](https://doi.org/10.5281/zenodo.11913042) in *if_segmentation.zip*.
diff --git a/molecular_heterogeneity_flow/README.md b/molecular_heterogeneity_flow/README.md
@@ -89,4 +89,4 @@ data
 ```
 
 ## Example data
-Example data to run this workflow can be found on [Zenodo]().
+Example data to run this workflow can be found on [Zenodo](https://doi.org/10.5281/zenodo.11913042) in *ly6g_heterogeneity.zip*.
diff --git a/molecular_signatures_flow/README.md b/molecular_signatures_flow/README.md
@@ -132,4 +132,4 @@ data
                     |   top_features.svg
 ```
 ## Example data
-Example data to run this workflow can be found on [Zenodo]().
+Example data to run this workflow can be found on [Zenodo](https://doi.org/10.5281/zenodo.11913042) in *ly6g_molecular_signatures.zip* or *ly6g_heterogeneity_signatures.zip*.
diff --git a/msi_if_registration_flow/README.md b/msi_if_registration_flow/README.md
@@ -95,4 +95,4 @@ data
 ```
 
 ## Example data
-Example data to run this workflow can be found on [Zenodo]().
+Example data to run this workflow can be found on [Zenodo](https://doi.org/10.5281/zenodo.11913042) in *msi_if_registration.zip*.
diff --git a/msi_preprocessing_flow/README.md b/msi_preprocessing_flow/README.md
@@ -141,4 +141,4 @@ data
 ```
 
 ## Example data
-Example data to run this workflow can be found on [Zenodo]().
+Example data to run this workflow can be found on [Zenodo](https://doi.org/10.5281/zenodo.11913042) in *maldi-2-group-sampleno.zip* containing raw MALDI-2 MSI data of bladder sections.
diff --git a/msi_segmentation_flow/README.md b/msi_segmentation_flow/README.md
@@ -79,4 +79,4 @@ data
 ```
 
 ## Example data
-Example data to run this workflow can be found on [Zenodo]().
+Example data to run this workflow can be found on [Zenodo](https://doi.org/10.5281/zenodo.11913042) in *msi_segmentation.zip*.
diff --git a/msiflow_env.yaml b/msiflow_env.yaml
@@ -1,139 +1,157 @@
-name: msiflow
+name: msiflow_env
 channels:
-  - conda-forge
   - defaults
 dependencies:
-  - bzip2=1.0.8=h10d778d_5
-  - ca-certificates=2024.6.2=h8857fd0_0
-  - libexpat=2.6.2=h73e2aa4_0
-  - libffi=3.4.2=h0d85af4_5
-  - libsqlite=3.46.0=h1b8f9f3_0
-  - libzlib=1.3.1=h87427d6_1
-  - ncurses=6.5=h5846eda_0
-  - openssl=3.3.1=h87427d6_0
-  - pip=24.0=pyhd8ed1ab_0
-  - python=3.12.3=h1411813_0_cpython
-  - readline=8.2=h9e318b2_1
-  - setuptools=70.0.0=pyhd8ed1ab_0
-  - tk=8.6.13=h1abcd95_1
-  - wheel=0.43.0=pyhd8ed1ab_1
-  - xz=5.2.6=h775f41a_0
+  - _libgcc_mutex=0.1=main
+  - _openmp_mutex=5.1=1_gnu
+  - bzip2=1.0.8=h5eee18b_6
+  - ca-certificates=2024.3.11=h06a4308_0
+  - expat=2.6.2=h6a678d5_0
+  - ld_impl_linux-64=2.38=h1181459_1
+  - libffi=3.4.4=h6a678d5_1
+  - libgcc-ng=11.2.0=h1234567_1
+  - libgomp=11.2.0=h1234567_1
+  - libstdcxx-ng=11.2.0=h1234567_1
+  - libuuid=1.41.5=h5eee18b_0
+  - ncurses=6.4=h6a678d5_0
+  - openssl=3.0.14=h5eee18b_0
+  - pip=24.0=py312h06a4308_0
+  - python=3.12.4=h5148396_1
+  - readline=8.2=h5eee18b_0
+  - setuptools=69.5.1=py312h06a4308_0
+  - sqlite=3.45.3=h5eee18b_0
+  - tk=8.6.14=h39e8969_0
+  - wheel=0.43.0=py312h06a4308_0
+  - xz=5.4.6=h5eee18b_1
+  - zlib=1.2.13=h5eee18b_1
   - pip:
-    - antspyx==0.4.2
-    - appdirs==1.4.4
-    - argparse-dataclass==2.0.0
-    - attrs==23.2.0
-    - catboost==1.2.5
-    - certifi==2024.6.2
-    - charset-normalizer==3.3.2
-    - chart-studio==1.1.0
-    - click==8.1.7
-    - cloudpickle==3.0.0
-    - conda-inject==1.3.2
-    - configargparse==1.7
-    - connection-pool==0.0.3
-    - contourpy==1.2.1
-    - cycler==0.12.1
-    - cython==0.29.37
-    - dask==2024.5.2
-    - datrie==0.8.2
-    - docutils==0.21.2
-    - dpath==2.2.0
-    - fastjsonschema==2.20.0
-    - fonttools==4.53.0
-    - fsspec==2024.6.0
-    - gitdb==4.0.11
-    - gitpython==3.1.43
-    - hdbscan==0.8.36
-    - humanfriendly==10.0
-    - idna==3.7
-    - imageio==2.34.1
-    - imbalanced-learn==0.12.3
-    - imblearn==0.0
-    - imgaug==0.4.0
-    - immutables==0.20
-    - imzy==0.2.6
-    - jinja2==3.1.4
-    - joblib==1.4.2
-    - jsonschema==4.22.0
-    - jsonschema-specifications==2023.12.1
-    - jupyter-core==5.7.2
-    - kiwisolver==1.4.5
-    - koyo==0.2.10
-    - lazy-loader==0.4
-    - lightgbm==4.3.0
-    - llvmlite==0.42.0
-    - locket==1.0.0
-    - loguru==0.7.2
-    - markupsafe==2.1.5
-    - matplotlib==3.8.4
-    - matplotlib-venn==0.11.10
-    - mpire==2.10.2
-    - natsort==8.4.0
-    - nbformat==5.10.4
-    - networkx==3.3
-    - nibabel==5.2.1
-    - numba==0.59.1
-    - numpy==1.26.4
-    - opencv-contrib-python==4.10.0.82
-    - opencv-python==4.10.0.82
-    - packaging==24.1
-    - pandas==2.2.2
-    - partd==1.4.2
-    - patsy==0.5.6
-    - pillow==10.3.0
-    - plac==1.4.3
-    - platformdirs==4.2.2
-    - plotly==5.22.0
-    - pluggy==1.5.0
-    - psutil==5.9.8
-    - pulp==2.8.0
-    - pygments==2.18.0
-    - pyimzml==1.5.4
-    - pynndescent==0.5.12
-    - pyparsing==3.1.2
-    - python-dateutil==2.9.0.post0
-    - python-graphviz==0.20.3
-    - pytz==2024.1
-    - pyyaml==6.0.1
-    - referencing==0.35.1
-    - requests==2.32.3
-    - reretry==0.11.8
-    - retrying==1.3.4
-    - rpds-py==0.18.1
-    - scikit-image==0.23.2
-    - scikit-learn==1.5.0
-    - scipy==1.13.1
-    - seaborn==0.13.2
-    - shap==0.45.1
-    - shapely==2.0.4
-    - six==1.16.0
-    - slicer==0.0.8
-    - smart-open==7.0.4
-    - smmap==5.0.1
-    - snakemake==8.13.0
-    - snakemake-interface-common==1.17.2
-    - snakemake-interface-executor-plugins==9.1.1
-    - snakemake-interface-report-plugins==1.0.0
-    - snakemake-interface-storage-plugins==3.2.2
-    - statsmodels==0.14.2
-    - stopit==1.1.2
-    - tabulate==0.9.0
-    - tenacity==8.3.0
-    - threadpoolctl==3.5.0
-    - throttler==1.2.2
-    - tifffile==2024.5.22
-    - toml==0.10.2
-    - toolz==0.12.1
-    - toposort==1.10
-    - tqdm==4.66.4
-    - traitlets==5.14.3
-    - tzdata==2024.1
-    - umap-learn==0.5.6
-    - urllib3==2.2.1
-    - webcolors==24.6.0
-    - wheezy-template==3.2.2
-    - wrapt==1.16.0
-    - xgboost==2.0.3
-    - yte==1.5.4
-prefix: /Users/philippaspangenberg/opt/anaconda3/envs/msiflow
+      - altair==5.3.0
+      - antspyx==0.4.2
+      - appdirs==1.4.4
+      - argparse-dataclass==2.0.0
+      - attrs==23.2.0
+      - blinker==1.8.2
+      - cachetools==5.3.3
+      - catboost==1.2.5
+      - certifi==2024.6.2
+      - charset-normalizer==3.3.2
+      - chart-studio==1.1.0
+      - click==8.1.7
+      - cloudpickle==3.0.0
+      - conda-inject==1.3.2
+      - configargparse==1.7
+      - connection-pool==0.0.3
+      - contourpy==1.2.1
+      - cycler==0.12.1
+      - cython==0.29.37
+      - dask==2024.5.2
+      - datrie==0.8.2
+      - docutils==0.21.2
+      - dpath==2.2.0
+      - fastjsonschema==2.20.0
+      - fonttools==4.53.0
+      - fsspec==2024.6.1
+      - gitdb==4.0.11
+      - gitpython==3.1.43
+      - hdbscan==0.8.36
+      - humanfriendly==10.0
+      - idna==3.7
+      - imageio==2.34.2
+      - imbalanced-learn==0.12.3
+      - imblearn==0.0
+      - imgaug==0.4.0
+      - immutables==0.20
+      - imzy==0.2.6
+      - jinja2==3.1.4
+      - joblib==1.4.2
+      - jsonschema==4.22.0
+      - jsonschema-specifications==2023.12.1
+      - jupyter-core==5.7.2
+      - kiwisolver==1.4.5
+      - koyo==0.2.10
+      - lazy-loader==0.4
+      - lightgbm==4.3.0
+      - llvmlite==0.42.0
+      - locket==1.0.0
+      - loguru==0.7.2
+      - markdown-it-py==3.0.0
+      - markupsafe==2.1.5
+      - matplotlib==3.8.4
+      - matplotlib-venn==0.11.10
+      - mdurl==0.1.2
+      - mpire==2.10.2
+      - natsort==8.4.0
+      - nbformat==5.10.4
+      - networkx==3.3
+      - nibabel==5.2.1
+      - numba==0.59.1
+      - numpy==1.26.4
+      - opencv-contrib-python==4.10.0.82
+      - opencv-python==4.10.0.84
+      - packaging==24.1
+      - pandas==2.1.4
+      - partd==1.4.2
+      - patsy==0.5.6
+      - pillow==10.3.0
+      - plac==1.4.3
+      - platformdirs==4.2.2
+      - plotly==5.22.0
+      - pluggy==1.5.0
+      - protobuf==4.25.3
+      - psutil==6.0.0
+      - pulp==2.8.0
+      - pyarrow==16.1.0
+      - pydeck==0.9.1
+      - pygments==2.18.0
+      - pyimzml==1.5.4
+      - pynndescent==0.5.13
+      - pyparsing==3.1.2
+      - python-dateutil==2.9.0.post0
+      - python-graphviz==0.20.3
+      - pytz==2024.1
+      - pyyaml==6.0.1
+      - referencing==0.35.1
+      - requests==2.32.3
+      - reretry==0.11.8
+      - retrying==1.3.4
+      - rich==13.7.1
+      - rpds-py==0.18.1
+      - scikit-image==0.23.2
+      - scikit-learn==1.5.0
+      - scipy==1.13.1
+      - seaborn==0.13.2
+      - shap==0.42.1
+      - shapely==2.0.4
+      - six==1.16.0
+      - slicer==0.0.7
+      - smart-open==7.0.4
+      - smmap==5.0.1
+      - snakemake==8.13.0
+      - snakemake-interface-common==1.17.2
+      - snakemake-interface-executor-plugins==9.1.1
+      - snakemake-interface-report-plugins==1.0.0
+      - snakemake-interface-storage-plugins==3.2.2
+      - statsmodels==0.14.2
+      - stopit==1.1.2
+      - streamlit==1.35.0
+      - tabulate==0.9.0
+      - tenacity==8.4.2
+      - threadpoolctl==3.5.0
+      - throttler==1.2.2
+      - tifffile==2024.5.22
+      - toml==0.10.2
+      - toolz==0.12.1
+      - toposort==1.10
+      - tornado==6.4.1
+      - tqdm==4.66.4
+      - traitlets==5.14.3
+      - typing-extensions==4.12.2
+      - tzdata==2024.1
+      - umap-learn==0.5.6
+      - urllib3==2.2.2
+      - watchdog==4.0.1
+      - webcolors==24.6.0
+      - wheezy-template==3.2.2
+      - wrapt==1.16.0
+      - xgboost==2.0.3
+      - yte==1.5.4
diff --git a/region_group_analysis_flow/README.md b/region_group_analysis_flow/README.md
@@ -101,4 +101,4 @@ data
 ```
 
 ## Example data
-Example data to run this workflow can be found on [Zenodo]().
+Example data to run this workflow can be found on [Zenodo](https://doi.org/10.5281/zenodo.11913042) in *region_group_analysis.zip*.