DOI: 10.15139/s3/fxohwv
title: Replication Data for: Turn-key mapping of cell receptor force orientation and magnitude using a commercial structured illumination microscope

description: This dataset supports the publication "Turn-key mapping of cell receptor force orientation and magnitude using a commercial structured illumination microscope" - Blanchard et al., Nature Communications, 2021 Raw SIM acquisitions, with corresponding background illumination correction images, of platelets (Figs. 1-2, 6, S3-7, S9, S12-13, S19), 3T3 Fibroblasts (Figs. 3, S8-9), and T-cells (Figs. 6, S19), as well as platelet timelapses (Figs. 5, S14, S16-18), are included here. Each SIM acquisition consists of a 3x3 (for 2D SIM) or 3x5 (for 3D SIM) montage of images in a single nd2 file. To view images, open them in Nikon Elements software or in Fiji (or ImageJ with the bioformats plugin installed). MATLAB code used to process data is included as a supplemental code with the publication at Nature Communications. Data is organized by experiment. The six experiments shown here should include all data used in the publication, but do not represent all data collected during the course of the study (some additional replicates were obtained to ensure reproducibility, but not quantitatively analyzed). Each experiment contains sub-directories that separate cells by surface, cell type, and, in some cases, cell number. The entire folders were uploaded, and contain many acquisitions that were ultimately not included in analysis due to poor signal-to-noise (among other reasons). Some folders include super-resolution reconstruction files, which are generally accompanied by text files that contain reconstruction metadata. Please use this dataset at your own risk, or consult with me if you have questions or ideas for how to use the data. Experiments 1 and 3 each contain batches of single-timepoint images of platelets. The “3D” images of both batches were pooled or used interchangeably for analyses shown in Figs. 1-2, 6, S3-7, S9, S12-13, S19. The representative platelet shown in Fig. 2 is from the file “Experiment 1/3D 10.nd2”. Experiments 1, 2, and 4 each contain folders batches of single-timepoint images of 3T3 fibroblasts. High signal-to-noise images were selected manually and pooled for analyses shown in Figs. 3, S8-9. The representative fibroblast shown in Fig. 3 is from the files in the folder “Experiment 4/3T3 Fibroblasts/Cell14_good”. The platelet timelapse data analyzed in Figs. 5, S14, and S16-18 are located in the folder “Experiment 4/Platelet Timelapses”. The folder contains three multipoint timelapse files. The files were collected sequentially, and contain the same set locations. Therefore, timelapse analysis would require stitching the three timelapse files together to obtain a single multipoint timelapse. The second timelapse was initiated ~4 minutes after the conclusion of the first timelapse, and the third timelapse was initiated ~2 minutes after the conclusion of the second timelapse. The T-cell data shown in Figs. 6, S19 is located in the folder “Tcell Experiment”. High signal-to-noise images were manually selected from the set of 3D and 2D SIM acquisitions in the folders corresponding to the third, fourth, and fifth surfaces. These selected cells were then pooled for analysis. The first and second surfaces did not produce high signal to noise images, hence why only brightfield (BF) images were collected.