82 Chapter 3 acids (referred to as starvation), which are essential for growth. This work is based on a previous study in which we demonstrated that long periods of amino-acid depletion lead to reduced growth of liver progenitor organoids20. Organoids in starvation medium, although coming from the same initial culture as the control ones, have impaired growth and smaller size due to the insult introduced at time point 0 H. To illustrate the results, these organoids have been tracked over time by imaging them every 24 H. In order to study the growth rate, 25 organoids for each medium were randomly selected and their cross-sectional areas were measured every 24 hours using brightfield images. Figure 2C demonstrates the growth at time point 0 and after 96 hours for organoids in control and starvation medium. Figure 2D demonstrates the area of those selected organoids over the experiment time. As it can be seen, the area of the organoids measured by OrganelX is very similar to those manually segmented especially for those in starvation medium. Only small differences of the areas are reported for those in the control medium after 48 hours. This is due to the fact that organoids are growing, their sizes increase over time, and OrganelX fails to quantify the size of such large organoids. This dissimilarity highlights the importance of continuously training OrganelX in order to optimize its response to bigger organoids. Publicly available data The e-Science website offers the tested data to be publicly available. Table 1 demonstrates the number of stacks in each file (S), the total number of detected organoids in the dome (O), as well as the average of all areas of the detected organoids in the dome (A) for the controlled and starvation medium. While OrganelX is able to measure more organoids than manual annotation, researchers have the option to select the organoids they are interested in. In this case, Table 1 also presents the organoids selected by a researcher (OMS) for a random selected stack (MS), in which small dying structures were not selected. The total average of those selected organoids is shown in the (AMS) column.
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