Phase contrast images of bacteria and ground truth segmentations

Name: Phase contrast images of bacteria Data type: Paired microscopy images and corresponding labels/masks used for model training, organized as recommended by the DenoiSeg documentation. Microscopy data type: Light microscopy (Phase Contrast) Manual annotations: Labels/masks obtained via manual segmentation. For each region, all cells were annotated manually. Uncertain objects were left unannotated. Microscope: Zeiss Axio Imager M2 epi-fluorescence microscope with a Zeiss Plan-Apochromat; 100x/1.4 oil DIC objective File format: .tif (float 32-bits for phase contrast and 16-bit for mask images) Image size: 256x256 pixels (Pixel size: 64.5 nm) Content: train - raw (33 files) - masks (33 files) test - raw (11 files) - masks (11 files) All images available in the raw folders were normalized by dividing the original images with a gaussian blurred version or the original image (200 pixels). A groovy code working within ImageJ/Fiji corresponding to this operation is as follow: ImagePlus normalize(ImagePlus input_image) { flatfield = (new Duplicator()).run(input_image) (new GaussianBlur()).blur(flatfield.getProcessor(), 200) return ImageCalculator.run(input_image, flatfield, "Divide create 32-bit") } import ij.ImagePlus import ij.plugin.Duplicator import ij.plugin.ImageCalculator import ij.plugin.filter.GaussianBlur