In vitro genotoxicity testing using γH2AX biomarker, Microscopy Dataset

• Main Authors: Křížkovská, Bára, Jablonská, Eva, Schätz, Martin
• Format: Dataset
• Language: English
• Published: 2023
• Subjects: Microscopy; BioImage Analysis; genotoxicity; γH2AX biomarke; In Vitro; Bia; Olympus; Turret; Orca
• Online Access: https://zenodo.org/record/7673199; https://doi.org/10.5281/zenodo.7673199

The Dataset was used and is supplementary to the paper "In vitro genotoxicity testing using γH2AX biomarker, microscopy and automatic image analysis in ImageJ - a pilot study with valinomycin". It contains both RAW single-channel images and numerical results obtained with BioImage Analysis and evaluation available through the GitHub repository: https://github.com/martinschatz-cz/genotoxicity-bia. Naming Convention for images ChannelName_YYYYMMD_Well_PossitionInWell_AcqRun.tiff Naming Convention for results Well_AllResults_YYYY-MM-DD_Results.csv The csv are ‘,’ separated, and automatically named by analysis script. Folder Structure Images (1069 files, as Images.zip) 4H - all images for all wells 24H - all images for all wells Results (36 files) Results_4H (as Results_4h.zip) Results_24H (as Results_24h.zip) Measurement Settings Manufacturer and model of microscope: Olympus IX83 P2ZF Objective lens magnification, NA: 10x Olympus IX3 Nosepiece, LensNA=0.3 Excitation filters (mounted in the light source) Violet: 395/25nm LED module 1, DAPI Green: 555/28nm LED module 5, Cy3 Quad band filter set for DAPI/FITC/Cy3/Cy5 Quad band polychroic mirror (mounted in the filter turret): BP 411-454nm, BP 495-536nm, BP 577-617nm BP 655-810nm Emission filters (mounted in the fast emission filter wheel, infront the camera): DAPI: BP 421-445nm Cy3: BP 581-619nm Illumination light source: Lumencor Lumencor Spectra X Lamp Pixel size: 650nm x 650nm Camera manufacturer and model: Hamamatsu ORCA-Flash4.0 Software program(s) and version: OLYMPUS cellSens Dimension 3.2 (Build 23706) Image acquisition settings expposure 500 ms gain: 0 binning: 4 x 4 Experiment manager: ZDC + autofocus, two channels: DAPI and Cy3 Image Processing and Analysis The data analysis workflow consists of several stages, each of which was executed by a specific script. Firstly, the raw data were manually cleaned and automatically sorted and organized using sort_wells.ijm in FIJI. Secondly, image analysis was performed using Process_WFolder_macro_v1.ijm in FIJI, which ...