Description of deposited data
This repository contains data and analysis code for the manuscript:
"Direct measurements of mRNA translation kinetics in living cells"	
Mikhail Metelev, Erik Lundin, Ivan L Volkov, Arvid H Gynnå, Johan Elf, and Magnus Johansson*	
Department of Cell and Molecular Biology, Uppsala University	
*Correspondence: m.johansson@icm.uu.se	

Update date: April 6, 2022

	Added DOI to published article

Update date: March 14, 2022


--Data--

Data is organized according to acquisition parameters (camera exposure frame time and temperature), strain and experiment type, and repetition number as:
"30ms/37C/L9/dataset1/"

Where each dataset folder contains the following folders and files:

- "RawData"
Original (raw) microscopy images. Within subfolders for each position (PosXX), corresponding to each imaged bacterial mini-colony, there are 3 phase contrast images taken with different Z offset (in folder A_Phase), a bright field image (B_Bf), and fluorescent images (C_553).

- "ImageAnalysisParameter"
TXT file with parameters used for image analysis, and TIFF file containing EMCCD camera offset image.

- "Output"
Preprocessed phase contrast images, cell segmentation masks and dot detection/tracking output data.

- "Output_HMM"
Tracking data output converted to HMM-pipeline format along with output of HMM analysis.

- "Output_TransMat"
Transformation matrix generated to transform phase contrast (cell segmentation) coordinates to fluorescence and bright field coordinates (required due to acquisition of data on different cameras).

- "SoftlinkedDataForAnalysis"
Soft links to the original raw microscopy images (from "RawData" folder) that are sorted by image positions. Used by the image analysis pipeline.

- "SoftlinkedDataToLookAt"
Soft links to the original raw microscopy images (from "RawData" folder), segmented images, and fluorescent images used for analysis that are sorted based on the type of the images to facilitate visual examination of images.


Each exposure time folder also includes one or several "HMMdata" folders, containing the results from the HMM analysis.

The data folders have been separated into several zip archives according to:

Data_5ms.zip					All 5 ms exposure data
Data_30ms_25C.zip				All 30 ms exposure data acquired at 25°C
Data_30ms_30C.zip				All 30 ms exposure data acquired at 30°C
Data_30ms_37C_h6_H98.zip			h6 and H98 data acquired at 30 ms and 37°C
Data_30ms_37C_h6-O.zip				h6 variants data acquired at 30 ms and 37°C
Data_30ms_37C_L9_S2.zip				L9 and S2 data acquired at 30 ms and 37°C
Data_30ms_37C_L9-AtaT-KSG_S2-AtaT-KSG.zip	L9 and S2 + AtaT or KSG acquired at 30 ms and 37°C
Data_30ms_HMM.zip	 			HMM results for all data acquired at 30 ms
Data_60ms.zip					All 60 ms exposure data


--Analysis code--
All analysis software, and code for figure generation, are included in the Software.zip archive

- "Figures_Tables"
Contains scripts to generate figures and data sheets from the data stored in the data zip archives.

- "Tools"
Contains the Image Analysis Pipeline ("ImAnalysis" folder) for processing of images obtained in microscopy experiments, plus additional analysis scripts.



--Licence--
CC BY 4.0

--Contact--
m.johansson@icm.uu.se