TY - JOUR T1 - SParticle, an algorithm for the analysis of filamentous microorganisms in submerged cultures JF - bioRxiv DO - 10.1101/159475 SP - 159475 AU - Joost Willemse AU - Ferhat Büke AU - Dino van Dissel AU - Sanne Grevink AU - Dennis Claessen AU - Gilles P. van Wezel Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/07/04/159475.abstract N2 - Streptomycetes are filamentous bacteria that produce a plethora of bioactive natural products and industrial enzymes. Their mycelial lifestyle typically results in high heterogeneity in bioreactors, with morphologies ranging from fragments and open mycelial mats to dense pellets. There is a strong correlation between morphology and production in submerged cultures, with small and open mycelia favoring enzyme production, while most antibiotics are produced mainly in pellets. Here we describe SParticle, a Streptomyces Particle analysis method that combines whole slide imaging with automated image analysis to characterize the morphology of submerged grown Streptomyces cultures. SParticle allows the analysis of over a thousand particles per hour, offering a high throughput method for the imaging and statistical analysis of mycelial morphologies. The software is available as a plugin for the open source software ImageJ and allows users to create custom filters for other microbes. Therefore, SParticle is a widely applicable tool for the analysis of filamentous microorganisms in submerged cultures.ARAspect ratioB&WBlack & whiteCfuColony forming unitscmcentimeterCOPASComplex Object Parametric Analyzer and SorterGbGigabytehhoursmLmilliliterMSMannitol soy flour agarnmnanometerRAMRandom access memoryROIRegion of interestRpmrounds per minuteTIFFtag image file formatTSBSTryptic soy broth with sucroseWSIWhole slide imagingµmmicrometer ER -