mastersthesis-code
Science Score: 44.0%
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○Scientific vocabulary similarity
Low similarity (10.8%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: Joel4Frei
- Language: Jupyter Notebook
- Default Branch: main
- Size: 33.2 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 1
Metadata Files
readme.md
Readme
Code collection used for Master's thesis.
Code are written and adapted for NIH3T3 cell line with optoFGFR and microscopy setup. There are four main experiments, two micropatterning codes, two viewers and additions including tools.
Experiments - Doseresponse Single stim on nucleus area to test sensitivity of optoFGFR. Includes shuffle of stim regimes. - Global/Local Two stimulations, one global (Nr.1) and one local (Nr.2). Stimulation areas along major axis of cell. - Directed Migration Novel stimulation mask tool, using 4 additional variables: - axis: 'y-axis' or 'x-axis' - type: 'outline' or 'surface' - direction: 'up-right' or 'down-left' - width: value in px (in case of 'outline' stim) - Bottom / Top Stimulation along major axis either on bottom or top with adjustable location on axis. New variable in stim regime called 'location' ('top' or 'bottom').
Micropatterns - Micropatterning Micropatterning requiring 1024x1024 mask. - Micropatterning DMD Novel approach using DMD px, thus image 600x800 mask.
Viewers - Dask Viewer Simple viewer of tiff image stacks of experiment including masks. - Superviewer Sophisticated viewer to load image stacks of experiment, descriptions of FOV/experiment and graph ERK graphs. Found in sperate repository (/super-viewer).
Additions - Required for pipeline - acquisition - stim - utils - semantic segmentation - Value Tinker window for easy stim regime input - Tools Include functions for mask creation and function to get next experiment number - Offset Calculate offset for stimulation - Mail Send mails during experiment for remote overview over exp status - Checklist Create checklist before exp start - Anch mask For bottom / top stimulation mask creation
Owner
- Login: Joel4Frei
- Kind: user
- Repositories: 1
- Profile: https://github.com/Joel4Frei
Citation (CITATION.cff)
cff-version: 1.2.0 message: "If you use this code, please cite it as below." authors: - family-names: "Frei" given-names: "Joël" title: "Master's Thesis Code" version: 1.0 doi: 10.5281/zenodo.10829952 date-released: 2024/03/18 url: "https://github.com/Joel4Frei/Mastersthesis-Code.git"