Multimodal Bioimaging Analysis Protocol

Data analysis was performed using the Zen analysis software (Carl Zeiss AG, Germany) as well as Fiji (ImageJ) [39 ]. Cell tracking was performed using the TrackMate plugin (v.2.8.2) for Fiji [40 (link)] and three-dimensional visualisations of the data were generated using the 3D Viewer (v.) plugin for Fiji [41 (link)]. The TrackMate [42 (link)] plugin for Fiji is a single particle tracking tool that identifies spots, i.e. cells, in every frame and the trajectories of cells are reconstructed by assigning an identity over these frames in the shape of a track. The positional data and numerical features generated using TrackMate were further processed and displayed using Matlab (R2014a, The Mathworks Inc., USA). Violin plots were generated using a script obtained via Matlab">https://github.com/bastibe/Violinplot-Matlab. The Mann-Whitney U procedure for statistical testing was run in Matlab. Multiview reconstruction was performed using the MultiView Reconstruction plugin in Fiji [43 , 44 (link)]. Object segmentation and volume calculation of the segments was done in Imaris (8.4.2, Bitplane AG, Switzerland).