# General description This data repository contains all the data, code and analysis objects used in the paper "Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization Elias Amselem*#, Bo Broadwater*, Tora Hävermark, Magnus Johansson & Johan Elf# Dept. Cell and Molecular Biology, Uppsala University, Sweden *Equal contribution #elias.amselem@icm.uu.se, johan.elf@icm.uu.se DOI: 10.17044/scilifelab.21602844 License: CC BY 4.0 This readme file was last updated: 2022-12-01 Preprint DOI_publication: https://doi.org/10.1101/2022.08.25.505330 " # Experimental data description Each zip file contains an experiment: 1) Tracking of beads standing still 20221115_EXP-22-BL9431_(Bead_StandingStill).zip Comment: Raw data, with analysis code and results. Alignment folder contains the PSF used for this experiment TriggerFacktor_Code includes the analysis code with the main file under the ProjectMain folder. The main file contains information on how to run and what plots are produced by the analysis. In the folder you also find main files configured to output data related to the figure in the file name. In the TriggerFactor_Code folder you will find the requirements.txt including all python dependencis with requiered version Folders xx_Bead_xxx are tracking instances with the structure: ScanData: Raw data Widefield: EMCCD image ow the FOV where the tracking has been performed zCam: raw data of the camera TIRF z-tracking Traj_xxx: analysis output as images. 2) Tracking of TF in WT and Mutant full pattern 20221025_EXP-22-BL9430_(TriggerFactorWT.Mutant_Beam(3x3p4)x3p3).zip Comment: Raw data, with analysis code and results. Alignment folder contains the PSF used for this experiment TriggerFactor_Code includes the analysis code with the main file under the ProjectMain folder. The main file contains information on how to run and what plots are produced by the analysis. In the folder you also find main files configured to output data related to the figure in the file name. In the TriggerFactor_Code folder you will find the requirements.txt including all python dependencis with requiered version Folders 6_WT_MLE_1.0_sn10 and 7_Mutant_MLE_1.0_sn10 are tracking of TF in E.coli with the folder structure: Positon ScanData: Raw data Widefield: EMCCD image of the FOV with cell segmentation mask zCam: raw data of the camera TIRF z-tracking Traj_xxx: analysis output as images. 3) Example analysis, 20220722_EXP-22-BL9428_Example_Analysis.zip Comment: See README file for instruction 4) Test of diffusion estimators 20220519_EXP-22-BL9418_(SimulationDiffusionTest).zip Comment: TriggerFactor_Code includes the analysis code with the main file under the ProjectMain folder. The main file contains information on how to run and what plots are produced by the analysis. In the folder you also find main files configured to output data related to the figure in the file name. Subfolders include results of different runs where w=window used, N=noise level used. In the article we are using the results of S_w16_N70nm_20periodes_2022_09_08 In the TriggerFactor_Code folder you will find the requirements.txt including all python dependencis with requiered version. 5) Simulation of the tracking within a E. coli like geometry, here the PSF used is the one obtain during the tracking experiment "20221025_EXP-22-BL9430_(TriggerFactorWT.Mutant_Beam(3x3p4)x3p3).zip" 20220429_EXP-22-BL9416_(SimulationMultibeam_PSF_20220106).zip Alignment folder contains the PSF used for this experiment Each folder contains a tracking simulation, either a fictive bead in a circular motion or as diffusion in a cell like geometry. In the ProjectMain folder you also find main files configured to output data related to the figure in the file name. In the TriggerFactor_Code folder you will find the requirements.txt including all python dependencis with requiered version. 6) Tracking of TF in WT and Mutant reduced pattern where we have removed the center shot 20220106_EXP-22-BL9417_(TriggerFactorMutant)_B(3x3p4)x3p3-1c).zip Alignment folder contains the PSF used for this experiment TriggerFactor_Code includes the analysis code with the main file under the ProjectMain folder. The main file contains information on how to run and what plots are produced by the analysis. In the ProjectMain folder you also find main files configured to output data related to the figure in the file name. In the TriggerFactor_Code folder you will find the requirements.txt including all python dependencis with requiered version. Folders 3_WT_Setting_(MLE_1_LongPSF_sn10) and 4_Mutant_Setting_(MLE_1_LongPSF_sn10) are tracking of TF in E.coli with the folder structure: Position ScanData: Raw data Widefield: EMCCD image of the FOV with cell segmentation mask zCam: raw data of the camera TIRF z-tracking Traj_xxx: analysis output as images. 7) Tracking of TF in WT and Mutant full pattern 20211111_EXP-21-BL9413_(TF_WT.Mutant)_B(3x3p4)x3p3.zip Alignment folder contains the PSF used for this experiment TriggerFactor_Code includes the analysis code with the main file under the ProjectMain folder. The main file contains information on how to run and what plots are produced by the analysis. In the ProjectMain folder you also find main files configured to output data related to the figure in the file name. In the TriggerFactor_Code folder you will find the requirements.txt including all python dependencis with requiered version. Folders 2_TriggerFactor_WT_MLE_1.0_sn10 and 3_TriggerFactor_Mutant_MLE_1.0_sn10 are tracking of TF in E.coli with the folder structure: Position ScanData: Raw data Widefield: EMCCD image of the FOV with cell segmentation mask zCam: raw data of the camera TIRF z-tracking Traj_xxx: analysis output as images. 8) Growth assay for in vivo function of TF-HaloTag File: 20221118_EXP-22-BZ0898_(Growth_assay_for_in_vivo_function_of_TF-HaloTag).zip Comment: Assessment of TF-HaloTag in vivo function. 9) Figure source data. All figures of the manuscript are here presented. In each folder, with name related to the figure, there is an INFO file describing the content. The INFO txt file describe which project the data is comming from, and under the Fig_data folder you will find csv files with the data. The name of each CSV file should give an indication of which part of the figure the data is related to. The first line in each csv file describes the data column and the unit of that column.