Abstract: Detection and analysis of biological particles can provide useful information with respect to a wide range of applications. Those include but are not limited to analysis of disease markers in diagnostic samples, quantification of bacteria and/or viral particles in environmental samples, and detection of specific proteins in cell culture samples. The methods presented herein provide simple, rapid and reliable means of detecting and analyzing biological particles in a hydrogel, and are especially suitable for quantification of for example nucleic acids, viral particles, bacteria, yeast, animal cells, and proteins. The invention also relates to a kit of parts and to a system for detection and analysis of biological particles in a hydrogel.