https://vladimir-vinarsky.me/notes/ Recent content in Notes on Vladimir Vinarsky Hugo -- 0.122.0 en-us Mon, 12 Aug 2024 18:14:20 +0200 https://vladimir-vinarsky.me/notes/sarcomere-cell-profiler-integration/ Mon, 12 Aug 2024 18:14:20 +0200 https://vladimir-vinarsky.me/notes/sarcomere-cell-profiler-integration/ Describe reproducibly how to integrate measurments of sarcomere, YAP1 intensity, and cardiomyocyte area How it was actually done before I have a table where I somehow connected the measurments from cell area supplied by Katka and the sarcomere measurments clear Outline Set up pipeline Run cells through pipeline Quality check Post process first part Tweak pipeline for the non-recognized cells Re-run cells through pipeline Quality check Post process second part Measure sarcomere length Process the treatmen_image-number_measurement-number Integrate with cell profiler measurements Set positivity treshold Split/label cells to positive/negative How to integrate multiple measurments of sarcomere length with a single value of cell area/yap1 intensity? https://vladimir-vinarsky.me/notes/git/ Mon, 01 Jan 0001 00:00:00 +0000 https://vladimir-vinarsky.me/notes/git/ Motivation Learn how to use GIT to be able to test different versions of scripts without a fear that I lose everything Resource ProGit book What I really need to learn! How to branch when I do some exploratory stuff how to go back to a state where things worked How to update/merge the new changes which are better than it was before How to label the most important changes (versioning? https://vladimir-vinarsky.me/notes/statistics/ Mon, 01 Jan 0001 00:00:00 +0000 https://vladimir-vinarsky.me/notes/statistics/ https://vladimir-vinarsky.me/notes/hugo/ Mon, 01 Jan 0001 00:00:00 +0000 https://vladimir-vinarsky.me/notes/hugo/ Github actions This means, you can run a virtual machine with linux commands to do somethind with your files Overall structure name: Convert Hugo Posts to PDF on: # This is to run the action manually workflow_dispatch: # this works when you cchange an post file called index.md push: paths: - 'content/**/index.md' jobs: convert: runs-on: ubuntu-latest permissions: # important in case you want to create new files contents: write steps: - name: Checkout repo uses: actions/checkout@v3 # install packages you need - name: Install pandoc and yq (for reading front matter) # install all run: | sudo apt-get update sudo apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-latex-recommended # Here run the actual code - name: make a backup file for each md file run: | set -e shopt -s globstar nullglob for file in content/**/index.