Software
We are continuously developing new computational solutions to provide novel tools and improve our day-to-day data throughput and quality. These solutions range from small shiny apps to more comprehensive pieces of software. A brief list is given below. Make sure to check our GitHub for a more comprehensive list and usage instructions!
ARCOS is a computational method to detect and quantify collective phenomena. The algorithm was designed with the signaling of epithelial cells in mind however it is also applicable to other systems even outside of the realm of cell biology.
CODEX is an approach for time-series data exploration that relies on Convolutional Neural Networks (CNNs). It is most useful for identifying signature dynamics in sets of heterogeneous trajectories. It was originally developed for the study of single-cell signaling data but can be applied to any time-series data.
The Led Illumination Tool for Optogenetic Stimulation (LITOS) can be used for the stimulation of cells containing an optogenetic system. A commercially available 32x64 RGB LED matrix is used to illuminate cells placed in various microplate formats (6 well up to 96 wells), petri dishes or cell culture flasks. The control unit for the LED matrix is a custom-built printed circuit board (PCB) containing a screen which shows relevant information during the illumination process.
An html-based plate viewer for microscopy images using DeepZoom technology.
Time Course Inspector (TCI) is a software for visualization, analysis and clustering of time-series. The driving philosophy is to provide a simple, yet flexible GUI to perform various time-series analyses without any programming knowledge. TCI is written as an R shiny web app which provides a reactive, fast and customizable framework to produce elegant visualizations.
A web-app for easy interactive clustering. Choose your clustering algortihms, play with parameters and plot results in a fully interactive fashion. The algortihms set include: classical hierarchical clustering, sparse hierarchical clustering and a model-based Bayesian approach tailored to cluster high-dimensional data (with many more variables than samples). FreeClust was published in Analytical Chemistry.
A custom script to control the 96 channels LED matrix from Life Cell Instrument. Here is an example of the layouts that can be obtained: https://www.youtube.com/watch?v=slNDvWbf6eY&feature=youtu.be.