the community site for and by developmental biologists
Posted by Joachim Goedhart on September 29th, 2020
The superplot was recently proposed as a data visualization strategy that improves the communication of experimental results (Lord et al, 2020). To simplify the visualization of data with a superplot, I created a web tool that is named SuperPlotsOfData (Goedhart, 2020). The superplot tutorial for R , the tutorial for Python and the SuperPlotsOfData web app use the[…]
Posted by Joachim Goedhart on May 6th, 2020
In a previous blog I explained how animated plots can be made to illustrate the dynamics of data. Animated plots go nicely together with the movies from which the data was extracted. Here, I explain how to display a movie and plot side-by-side, starting from a stack of images and using only open source software.[…]
Posted by Joachim Goedhart on April 27th, 2020
Data from time-lapse experiments is often displayed in a graph or plot, to visualize the dynamics of biological systems (Goedhart, 2020). Ironically, the perception of the dynamics is largely lost in a static plot. That’s where animated plots come in. Animated plots are a great way to display the dynamics of the underlying data. Below, I[…]
Posted by Joachim Goedhart on August 29th, 2019
The importance of barrier-free use of colors in images and graphs has been highlighted in letters to editors (Miall, 2007), papers (Geissbuehler and Lasser, 2013, Levine, 2009), editorials (anonymous, 2007), columns (Wong, 2011) and on numerous web pages. One of the recommendations is to use a color blindness simulator. Having a color vision deficiency myself,[…]
Posted by Joachim Goedhart on June 25th, 2019
In a previous blog, I have highlighted several ways to visualize the cell-to-cell heterogeneity from time-lapse imaging data. However, I have ignored that data is often rescaled in a way that reduces variability. For time-lapse imaging data, it is common to set the initial fluorescence intensity to 1 (or 100%). As a consequence, any changes[…]
Posted by Joachim Goedhart on February 13th, 2019
A good statistic is the one that you can understand. Mean values are understandable and everybody knows how to calculate them. Most people also realize how the mean value can be skewed by an outlier. So we know what the mean represents and we are aware of its limitations. In sharp contrast, the Null Hypothesis[…]
Posted by Joachim Goedhart on February 3rd, 2019
Last year, I started to experiment with signing my reports for peer review of manuscripts, inspired by other people on twitter (@kaymtye, @AndrewPlested who in turn were inspired by Leslie Voshall). This year, the experiment is a bit different. I will only review for journals that allow non-anonymous peer-review. Why? That was the question raised[…]
Posted by Joachim Goedhart on December 12th, 2018
When we examined the kinetics of Rho GTPase activity in endothelial cells in response to receptor stimulation (Reinhard, 2017), we noticed considerable cell-to-cell heterogeneity. In the original work we published graphs with the average response, reflecting the response of the whole cell population. However, these graphs fail to show the cellular heterogeneity. What is the[…]
Posted by Joachim Goedhart on October 8th, 2018
Calculation and reporting of p-values is common in scientific publications and presentations (Cristea and Ioannidis, 2018). Usually, the p-value is calculated to decide whether two conditions, e.g. control and treatment, are different. Although a p-value can flag differences, it cannot quantify the difference itself (footnote 1). Therefore, p-values fail to answer a very relevant question:[…]
Posted by Joachim Goedhart on June 26th, 2018
Experiments are rarely performed in isolation. Usually, several conditions are compared in parallel or sequential experiments. This experimental strategy also applies to time-dependent data, e.g. from timelapse imaging. So, naturally, after I published a ‘walk-through for plotting temporal data using R and ggplot2, I was immediately asked how to plot two (or more) sets of[…]
