TY - DATA AB - Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here, we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease. AU - Danzl, Johann G ID - 13126 TI - Research data for the publication "Imaging brain tissue architecture across millimeter to nanometer scales" ER - TY - DATA AB - Script to perform a simple exponential lifetime fit of a ROI on time stacks acquired with a FLIM X16 TCSPC detector (+example data) AU - Hauschild, Robert ID - 5588 KW - FLIM KW - FRET KW - fluorescence lifetime imaging TI - Fluorescence lifetime analysis of FLIM X16 TCSPC data ER - TY - DATA AB - Matlab script to calculate the forward migration indexes (/) from TrackMate spot-statistics files. AU - Hauschild, Robert ID - 5570 KW - Cell migration KW - tracking KW - forward migration index KW - FMI TI - Forward migration indexes ER - TY - DATA AB - This repository contains the data collected for the manuscript "Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity". The data is compressed into a single archive. Within the archive, different folders correspond to figures of the main text and the SI of the related publication. Data is saved as plain text, with each folder containing a separate readme file describing the format. Typically, the data is from fluorescence microscopy measurements of single cells growing in a microfluidic "mother machine" device, and consists of relevant values (primarily arbitrary unit or normalized fluorescence measurements, and division times / growth rates) after raw microscopy images have been processed, segmented, and their features extracted, as described in the methods section of the related publication. AU - Bergmiller, Tobias AU - Andersson, Anna M AU - Tomasek, Kathrin AU - Balleza, Enrique AU - Kiviet, Daniel AU - Hauschild, Robert AU - Tkacik, Gasper AU - Guet, Calin C ID - 5560 KW - single cell microscopy KW - mother machine microfluidic device KW - AcrAB-TolC pump KW - multi-drug efflux KW - Escherichia coli TI - Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity ER - TY - DATA AB - One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. The Video is licensed under a CC BY NC ND license. AU - Von Wangenheim, Daniel AU - Hauschild, Robert AU - Friml, JirĂ­ ID - 5565 TI - Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel ER - TY - DATA AB - Current minimal version of TipTracker AU - Hauschild, Robert ID - 5566 KW - tool KW - tracking KW - confocal microscopy TI - Live tracking of moving samples in confocal microscopy for vertically grown roots ER - TY - DATA AB - This FIJI script calculates the population average of the migration speed as a function of time of all cells from wide field microscopy movies. AU - Hauschild, Robert ID - 5555 KW - cell migration KW - wide field microscopy KW - FIJI TI - Fiji script to determine average speed and direction of migration of cells ER -