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Rebecca Senft With slide scanners and other automated, high-throughput microscopes becoming more and more common, it’s important to understand how to work with the large image files they produce. Whole slide file formats (e.g., .mrxs, .svslide, .svs, .vms) are often massive when uncompressed (>40 GB...

Fernanda Garcia-Fossa & Anne Carpenter In a typical quantitative microscopy experiment, biologists choose fluorescent biomarkers and measure particular features (that is “metrics”) that they hypothesize will be perturbed in their samples. But in image-based profiling, you aim to let the cells tell...

Mario Costa Cruz If you have color images stained with light-absorbing dyes, the UnmixColors module might be able to separate the dyes into separate channels so that they can be analyzed separately. Separating the dyes into channels can be a difficult task with traditional methods such as split...