Batch spots detections and statistics
Institution: Institut Pasteur
Please cite as: Louveaux, Marion. (2020, July 1). Batch spots detections and statistics (Version 1.0). Zenodo. http://doi.org/10.5281/zenodo.3925263
Test image available at doi: 10.5281/zenodo.3925213 (choose the HeLa cell example).
This protocol detects spots and extract measurements from spot ROIs. It loops over a folder of input images.
In the folder block, provide the path to the folder containing the images to process. The protocol is designed to process .czi images. The results folder path is derived from this input folder path.
On each .czi image, this protocol:
1. gets the ROI drawned manually to delimit the nuclei with the Polygon ROI tool
2. extracts the green channel and apply a median filter of half size = 1
3. applies the Spot Detector with a scale of 1 (sensitivity to 55) on the nuclear ROI only.
4. measures spots properties with the ROI Statistics block
5. exports Spots measurements of mean fluorescence intensity as .csv
6. exports the results of the inclusion analysis (which spot is contained in which nucleus) as .csv (second file)