Devel

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,38 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/codeql-analysis.yml

@@ -0,0 +1,71 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ master ]
+  schedule:
+    - cron: '27 16 * * 1'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'cpp', 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python' ]
+        # Learn more:
+        # https://docs.github.com/en/free-pro-team@latest/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning#changing-the-languages-that-are-analyzed
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v1
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v1
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    #- run: |
+    #   make bootstrap
+    #   make release
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v1

.gitignore

@@ -37,3 +37,15 @@
 .Trashes
 ehthumbs.db
 Thumbs.db
+_gsdata_/*
+
+# UPGRADE STUDY #
+######################
+# We want to exclude *input* and *output* images (i.e. tiles, NDPI, TIFs); 
+# these are 1) personal data, and 2) too large.
+upgrade_study/*
+upgrade_study/_temp/*
+upgrade_study/CD68/*
+upgrade_study/EVG/*
+upgrade_study/SMA/*
+.DS_Store

LICENSE

@@ -1,5 +1,8 @@
 The MIT License (MIT) <http://opensource.org/licenses/MIT>
-Copyright (c) 2014-2015, UMC Utrecht, Bas Nelissen
+Copyright (c) 2014-2021, 
+Bas G.L. Nelissen (https://github.com/bglnelissen),
+Sander W. van der Laan (https://github.com/swvanderlaan), 
+UMC Utrecht, Utrecht, the Netherlands.
 
 Permission is hereby granted, free of charge, to any person obtaining a
 copy of this software and associated documentation files (the
@@ -18,4 +21,4 @@ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
 IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
 CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
 TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
-SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

README.md

@@ -1,22 +1,39 @@
-[slideToolkit](http://bglnelissen.github.io/slideToolkit)
+[slideToolKit](https://github.com/swvanderlaan/slideToolKit)<img align="right" height="200" src=images/slideToolKit_logo_print_transparent.png>
 ============
 
-####_slideToolkit: an assistive toolset for the histological quantification of whole slide images_
+**slideToolKit**: _an assistive toolset for the histological quantification of whole slide images_
 
 The demand for accurate and reproducible phenotyping of a disease trait increases with the rising number of biobanks and genome wide association studies. Detailed analysis of histology is a powerful way of phenotyping human tissues. Nonetheless, purely visual assessment of histological slides is time-consuming and liable to sampling variation and optical illusions and thereby observer variation, and external validation may be cumbersome. Therefore, computerized quantification of digitized histological slides is often preferred as a more precise and reproducible, and sometimes more sensitive approach. Relatively few free toolkits are, however, available for fully digitized microscopic slides, usually known as whole slides images.
 
-In order to comply with this need, we developed the slideToolkit as a fast method to handle large quantities of low contrast whole slides images using advanced cell detecting algorithms. The slideToolkit has been developed for modern personal computers and high-performance clusters (HPCs) and is available as an open-source project on github.com.
+In order to comply with this need, we developed the **slideToolKit** as a fast method to handle large quantities of low contrast whole slides images using advanced cell detecting algorithms. At the core **slideToolKit** uses [CellProfiler](http://cellprofiler.org) to analyze the whole slide images efficiently. The **slideToolKit** has been developed for modern personal computers (macOS, Ubuntu) and high-performance clusters (HPCs) and is available as an open-source project on [GitHub](https://swvanderlaan.github.io/slideToolKit/).
 
-A workflow consists of four consecutive steps. In the first step (acquisition), whole slide images are collected and converted to TIFF files. In the second step (preparation), files are organized. The third step (tiles), creates multiple manageable tiles to count. In the fourth step (analysis), tissue is analyzed and results are stored in a data set. Using this method, two consecutive measurements of 303 slides showed an intraclass correlation of 0.99.
+A typical [workflow](images/slideToolkit.workflow.png) consists of four consecutive steps. 
+- In the first step (acquisition), whole slide images are collected and converted to TIFF files. 
+- In the second step (preparation), files are organized. 
+- The third step (tiles), creates multiple manageable tiles to count. 
+- In the fourth step (analysis), tissue is analyzed and results are stored in a data set. Using this method, two consecutive measurements of 303 slides showed an intraclass correlation of 0.99 ([Vrijenhoek J.E.P. _et al._](https://www.ncbi.nlm.nih.gov/pubmed/25541691)).
 
-In conclusion, slideToolkit provides a free, powerful and versatile collection of tools for automated feature analysis of whole slide images to create reproducible and meaningful phenotypic datasets.
 
------------------------------------------------
-Citation: Nelissen BGL, van Herwaarden JA, Moll FL, van Diest PJ, Pasterkamp G (2014) <i>SlideToolkit: An Assistive Toolset for the Histological Quantification of Whole Slide Images.</i> <bold>PLoS ONE 9(11): e110289</bold>. doi:10.1371/journal.pone.0110289. 
-Direct link: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0110289.
+<img align="center" width="400" height="314" src=images/slideToolkit.workflow.small.png>
+
+_The slideToolKit workflow._
+
+In conclusion, **slideToolKit** provides a free, powerful and versatile collection of tools for automated feature analysis of whole slide images to create reproducible and meaningful phenotypic datasets.
+
+
+#### Instructions and usage
+Detailed instructions on using **slideToolKit** can be found in the [wiki](https://github.com/swvanderlaan/slideToolKit/wiki).
+
+
+#### Citations
+- Nelissen B.G.L., van Herwaarden J.A., Moll F.L., van Diest P.J., and Pasterkamp G. (2014) _SlideToolkit: An Assistive Toolset for the Histological Quantification of Whole Slide Images._ **PLoS One.** 2014 Nov 5;9(11):e110289. doi: 10.1371/journal.pone.0110289. [Direct link](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0110289).
+- Vrijenhoek J.E.P., Nelissen B.G.L., Velema E., Vons K., de Vries J.P.P.M., Eijkemans M.J.C., den Ruijter H.M., de Borst G.J., Moll F.L., and Pasterkamp G (2014) _High Reproducibility of Histological Characterization by Whole Virtual Slide Quantification; An Example Using Carotid Plaque Specimens._ **PLoS One**. 2014 Dec 26;9(12):e115907. doi: 10.1371/journal.pone.0115907. [Direct link](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115907).
+- Mekke J.M., Sakkers T.R., Verwer M.C., van den Dungen N.A.M, Song Y., Miller C., Pasterkamp G., Mokry M., den Ruijter H.M., de Kleijn D.P.V., de Borst G.J., Haitjema S., and van der Laan S.W. _Glycophorin C in atherosclerotic plaque is associated with major adverse cardiovascular events after carotid endarterectomy_ preprint **medRxiv** 2021.07.15.21260570; doi: [https://doi.org/10.1101/2021.07.15.21260570](https://doi.org/10.1101/2021.07.15.21260570)
 
-The MIT License (MIT): <http://opensource.org/licenses/MIT>.
-Copyright (c) 2014-2016, Bas G.L. Nelissen, UMC Utrecht, the Netherlands.
 
 -----------------------------------------------
-> Installation instructions for Ubuntu and Mac OS X Mountain Lion+ can be found in [guides](guides).
+#### Licence
+The MIT License (MIT): <http://opensource.org/licenses/MIT>.
+
+Copyright (c) 2014-2021, [Bas G.L. Nelissen](https://github.com/bglnelissen) & [Sander W. van der Laan](https://github.com/swvanderlaan), UMC Utrecht, Utrecht, the Netherlands.
+

conda_yml/anaconda3_8_2021_05_cp413.v2.yml

@@ -0,0 +1,51 @@
+# run: conda env create -f anaconda3_8_2021_05_cp413.v2.yml
+# run: conda env update -f anaconda3_8_2021_05_cp413.v2.yml
+# run: conda env remove -n cp4
+name: cp4
+
+channels:
+- conda-forge
+- anaconda
+- bioconda
+- defaults
+
+dependencies:
+- python=3.8
+- pip
+- numpy
+- matplotlib
+- pandas
+- mysqlclient
+- openjdk
+- scikit-learn
+- mahotas
+- gtk2
+- Jinja2=3.0.1
+- inflect=5.3.0
+- wxpython=4.1.0
+- mysqlclient=1.4.4
+- sentry-sdk=0.18.0
+- bftools
+- cairo
+- freetype
+- gettext
+- giflib
+- gtk2
+- gtk3
+- imagemagick
+- java-jdk
+- jpeg
+- wmctrl
+- zbar
+- tclap
+- pip:
+    - cellprofiler==4.1.3
+    - arrow
+    - pathlib
+    - opencv-contrib-python
+    - openslide-python>=1.1.2
+
+# you could automatically provide the prefix, or just do it via the prompt
+# prefix: ~/anaconda3/envs/cp4
+
+# prefix: /Users/[username]/anaconda3/envs/cp4

conda_yml/conda3_8_cp413.v1.yml

@@ -0,0 +1,51 @@
+# run: conda env create -f conda3_8_cp413.v1.yml
+# run: conda env update -f conda3_8_cp413.v1.yml
+# run: conda env remove -n cp4
+name: cp4
+
+channels:
+- conda-forge
+- miniconda
+- bioconda
+- defaults
+
+dependencies:
+- python=3.8
+- pip
+- numpy
+- matplotlib
+- pandas
+- mysqlclient
+- openjdk
+- scikit-learn
+- mahotas
+- gtk2
+- Jinja2=3.0.1
+- inflect=5.3.0
+- wxpython=4.1.0
+- mysqlclient=1.4.4
+- sentry-sdk=0.18.0
+- bftools
+- cairo
+- freetype
+- gettext
+- giflib
+- gtk2
+- gtk3
+- imagemagick
+- java-jdk
+- jpeg
+- wmctrl
+- zbar
+- tclap
+- pip:
+    - cellprofiler==4.1.3
+    - arrow
+    - pathlib
+    - opencv-contrib-python
+    - openslide-python>=1.1.2
+
+# you could automatically provide the prefix, or just do it via the prompt
+# prefix: ~/miniconda3/envs/cp4
+
+# prefix: /Users/[username]/miniconda3/envs/cp4

examples/README.md

@@ -1,7 +1,7 @@
-[Examples](http://bglnelissen.github.io/slideToolkit)
+[Examples](http://swvanderlaan.github.io/slideToolkit)
 ============
 
-An example pipeline made with CellProfiler is provided.
+A couple of example pipelines made with CellProfiler are provided.
 
 -----------------------------------------------
 > Installation instructions can be found in [guides](guides).