DOI: 10.25824/redu/njwobd
title: High content analysis of colloidal silver in Huh-7 cells

description: Live Cell Painting Dataset This package includes all output data and accompanying documentation generated during a high-content analysis (HCA) study investigating morphological changes in Huh7 cells exposed to colloidal silver formulations. The research was conducted as part of Bruno Losi Menna’s Master’s work at the NanoCell Interactions Laboratory, University of Campinas (UNICAMP). Dyes: Acridine Orange, Calcein/Hoechst Directory Structure ├── AcridineOrange_PrataReal │ ├── Data_File │ ├── Data_Normalized │ ├── Notebooks │ ├── Output │ └── Platemaps ├── AcridineOrange_PrataReal_Images ├── AcridineOrange_PrataReal_Tools │ ├── CellPose │ ├── CellProfiler ├── AcridineOrange_Almacura_PrataVida │ ├── Data_File │ ├── Data_Normalized │ ├── Morpheus_data │ ├── Notebooks │ ├── Output │ └── Platemaps ├── AcridineOrange_Almacura_PrataVida_Images ├── AcridineOrange_Almacura_PrataVida_Tools │ ├── CellPose │ ├── CellProfiler ├── CalceinHoechst_PrataVida │ ├── Data_File │ ├── Data_Normalized │ ├── Morpheus_data │ ├── Notebooks │ ├── Output │ └── Platemaps ├── CalceinHoechst_PrataVida_Images ├── CalceinHoechst_PrataVida_Tools │ ├── CellPose │ └── CellProfiler Folder Description AcridineOrange_PrataReal This folder contains all the experimental data and analyses related to the use of colloidal silver (Prata Real) in conjunction with Acridine Orange staining. Data_File: Contains the raw experimental data generated using CellProfiler (version 2.2.3). Data_Normalized: Contains the normalized data file, processed using the data normalization templates provided in the Notebooks folder. Notebooks: Contains data processing templates for normalization, aggregation, annotation, and feature selection. Output: Contains the final processed file generated using the notebooks. Platemap: Contains the layout of the 96-well plate used during image acquisition. AcridineOrange_PrataReal_Images This folder contains all the Images related to the use of colloidal silver (Prata Real) in conjunction with Acridine Orange staining. These folders are further subdivided into two independent replicate folders, each containing a subfolder named 'load_data_csv', which holds the information for each image required for CellProfiler analysis. Acridine Orange images were acquired using a 20× objective on the Cytation 5 imaging system. Image acquisition utilized the following LED cube channels: GFP channel (excitation/emission = 469/525 nm) for the visualization of nuclei, nucleoli, and cytoplasm; PI channel (excitation/emission = 531/647 nm) for the detection of acidic vesicles. AcridineOrange_PrataReal_Tools This folder contains all files related to the application of trained models using Cellpose (version 2.2.3) and analysis pipelines developed in CellProfiler (version 4.2.5). AssayDev: To evaluate segmentation consistency across the plate, a CellProfiler pipeline was created to process and save outlines from a single representative site in each well. Cellprofiler_file: Contains the CellProfiler pipeline used for image analysis. Plate_Cell_Outlines_cells: Stores the segmentation outline images for whole cells, generated by CellProfiler. Each image corresponds to one selected site per well and is used to visually assess the accuracy of cell segmentation. Plate_Cell_Outlines_nuclei: Stores the segmentation outline images for nuclei, generated by CellProfiler. Each image corresponds to one selected site per well and is used to visually assess the accuracy of nuclei segmentation. Quality_Control: Image quality control was performed using CellProfiler Analyst (v3.0.4), excluding out-of-focus images and those with artifacts. Spreadsheet: Contains tabular data exported from the CellProfiler pipeline. AcridineOrange_Almacura_PrataVida This folder contains all the experimental data and analyses related to the use of colloidal silver (Almacura and Prata Vida) in conjunction with Acridine Orange staining. Data_File: Contains the raw experimental data generated using CellProfiler (version 2.2.3). Data_Normalized: This folder contains the normalized data files, processed using the data normalization templates provided within each experiment folder. Each experiment folder also includes the corresponding platemap detailing the layout of the 96-well plate used during image acquisition. Morpheus_data: Using the Morpheus online tool, features with a p-value 0.05 were selected for a comparative analysis. Notebooks: Contains data processing templates for normalization, aggregation, annotation, and feature selection. Output: Contains the final processed file generated using the notebooks. AcridineOrange_Almacura_PrataVida_Images This folder contains all the Images related to the use of colloidal silver (Almacura and Prata Vida) in conjunction with Acridine Orange staining. These folders are further subdivided into two independent replicate folders, each containing a subfolder named 'load_data_csv', which holds the information for each image required for CellProfiler analysis. Acridine Orange images were acquired using a 20× objective on the Cytation 5 imaging system. Image acquisition utilized the following LED cube channels: GFP channel (excitation/emission = 469/525 nm) for the visualization of nuclei, nucleoli, and cytoplasm; PI channel (excitation/emission = 531/647 nm) for the detection of acidic vesicles. AcridineOrange_Almacura_PrataVida_Tools This folder contains all files related to the application of trained models using Cellpose (version 2.2.3) and analysis pipelines developed in CellProfiler (version 4.2.5). AssayDev: To evaluate segmentation consistency across the plate, a CellProfiler pipeline was created to process and save outlines from a single representative site in each well. Cellprofiler_file: Contains the CellProfiler pipeline used for image analysis. Plate_Cell_Outlines_cells: Stores the segmentation outline images for whole cells, generated by CellProfiler. Each image corresponds to one selected site per well and is used to visually assess the accuracy of cell segmentation. Plate_Cell_Outlines_nuclei: Stores the segmentation outline images for nuclei, generated by CellProfiler. Each image corresponds to one selected site per well and is used to visually assess the accuracy of nuclei segmentation. Quality_Control: Image quality control was performed using CellProfiler Analyst (v3.0.4), excluding out-of-focus images and those with artifacts. Spreadsheet: Contains tabular data exported from the CellProfiler pipeline. CalceinHoechst_PrataVida This folder contains all the experimental data and analyses related to the use of colloidal silver (Prata Vida) in conjunction with Calcein/Hoechst staining. Data_File: Contains the raw experimental data generated using CellProfiler (version 2.2.3). Data_Normalized: This folder contains the normalized data files, processed using the data normalization templates provided within each experiment folder. Each experiment folder also includes the corresponding platemap detailing the layout of the 96-well plate used during image acquisition. Morpheus_data: Using the Morpheus online tool, features with a p-value 0.05 were selected for a comparative analysis. Notebooks: Contains data processing templates for normalization, aggregation, annotation, and feature selection. Output: Contains the final processed file generated using the notebooks. CalceinHoechst_PrataVida_Images This folder contains all the Images related to the use of colloidal silver (Prata Vida) in conjunction with Calcein/Hoechst staining. These folders are further subdivided into two independent replicate folders, each containing a subfolder named 'load_data_csv', which holds the information for each image required for CellProfiler analysis. Calcein/Hoechst images were acquired using a 20× objective on the Cytation 5 imaging system. Image acquisition utilized the following LED cube channels: GFP channel (excitation/emission = 469/525 nm) for the visualization of nuclei; DAPI channel (excitation/emission = 377/447 nm) for the visualization of cytoplasm. CalceinHoechst_PrataVida_Tools This folder contains all files related to the application of trained models using Cellpose (version 2.2.3) and analysis pipelines developed in CellProfiler (version 4.2.5). AssayDev: To evaluate segmentation consistency across the plate, a CellProfiler pipeline was created to process and save outlines from a single representative site in each well. Cellprofiler_file: Contains the CellProfiler pipeline used for image analysis. Plate_Cell_Outlines_cells: Stores the segmentation outline images for whole cells, generated by CellProfiler. Each image corresponds to one selected site per well and is used to visually assess the accuracy of cell segmentation. Plate_Cell_Outlines_nuclei: Stores the segmentation outline images for nuclei, generated by CellProfiler. Each image corresponds to one selected site per well and is used to visually assess the accuracy of nuclei segmentation. Quality_Control: Image quality control was performed using CellProfiler Analyst (v3.0.4), excluding out-of-focus images and those with artifacts. Spreadsheet: Contains tabular data exported from the CellProfiler pipeline.