CellColoc example data

Example data for CellColoc This Zenodo record contains example data for testing and demonstrating CellColoc, a workflow for image-based cell and marker colocalization analysis. The dataset includes fluorescence microscopy example images with multiple channels that can be used to demonstrate channel handling, marker assignment, region inspection, and basic colocalization-oriented analysis workflows. Dataset contents The repository contains two types of example data: CellColoc example data provided by the authors of this repository, including multichannel fluorescence microscopy images for testing CellColoc. Redistributed example image data from Rathar (2018), originally published on Zenodo under the Creative Commons Attribution 4.0 International license. The Rathar dataset is included as additional example material for testing and demonstration purposes. Example CellColoc image Example filename: 250703_ID22488_CA1_tdTom_DAPI_IBA1_20x.czi This example image contains three fluorescence channels: Channel Marker Description 0 Cx3cr1-tdTomato Genetically labelled CX3CR1-positive cells. In brain parenchyma, these are expected to be predominantly microglia. 1 Iba1 immunostaining Microglia / macrophage-lineage marker. Used as an independent marker for microglia-like cells. 2 DAPI Nuclear stain Labels nuclei of all cells and is used for anatomical orientation and quality control. The intended marker comparison in this example is between Cx3cr1-tdTomato and Iba1. The DAPI channel is included mainly for anatomical orientation, tissue quality control, and optional support for region-of-interest definition or nuclear segmentation. Biological context of the CellColoc example image The tdTomato signal is interpreted as reporter expression in recombined CX3CR1-positive cells, for example in the context of a tamoxifen-inducible Cx3cr1-CreERT2 reporter system. The Iba1 signal is an independent immunostaining marker for microglia / macrophage-lineage cells. In this example dataset, the two channels can therefore be used to inspect whether tdTomato-positive cells are also Iba1-positive. Redistributed Zenodo example data from Rathar (2018) This repository also includes example image data from: Rathar, Raissa. “DAPI stained nuclei more or less clustered.” Zenodo, Version 1.0.0, 2018.DOI: 10.5281/zenodo.1304211Original source: https://doi.org/10.5281/zenodo.1304211License: Creative Commons Attribution 4.0 International, CC BY 4.0. The Rathar dataset contains fluorescence microscopy images of DAPI-stained nuclei and corresponding TexasRed-stained cells. The files are redistributed here as example data for testing CellColoc. Changes Modifications to the Rathar dataset files, if any, are limited to file selection, file organization, and integration into the CellColoc example-data structure. The biological image content of the original Rathar files was not intentionally altered unless explicitly stated in the file-level metadata or accompanying documentation. Attribution and license information Files originating from Rathar (2018) are redistributed under the terms of the Creative Commons Attribution 4.0 International license. Please cite the original dataset when using these files: Rathar, Raissa. “DAPI stained nuclei more or less clustered.” Zenodo, 2018. DOI: 10.5281/zenodo.1304211. The remaining files in this repository were provided as CellColoc example data by the authors of this repository. Please cite this Zenodo repositroy when using these files. Intended use These data are intended for: testing CellColoc installation and input handling; demonstrating multichannel fluorescence image loading; testing marker-channel assignment; demonstrating example colocalization workflows; validating example analysis scripts and tutorials. These files are provided as example data and should not be interpreted as a complete biological study.