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Akhtar_​et_​al_​Bacterial_​FISH_​Example_​Workflow

This workflow accompanies the manuscript of Akhtarand Stewart et. al. It is meant to perform an imagesegmentation of microscopic images with multicolorstainings to detect bacteria via fluorescent in situHybridization (FISH). The exemplary workflow usesimages recorded by a Zeiss LSM710 microscopewith a blue and a red fluorophor. If anothermicroscopic system and/or other fluorophores areused, the pipeline needs to be adjusted accordingly. Load imagesSplit clumps(Fluorophor I/ Column I)Split clumps(Fluorophor II/ Column II)Filter the columnsMerge data streamsConvert to Byte TypeSplit channelsMerge data streamsDetect connected componentsRename the columnsCount selected / gated cell populationCalculate fraction of doublelabeled cellsRename columnsCombine channelsFilter featuresSave result images as jpegConvert to RGBIndividual Segmentation AIndividual Segmentation B Image Reader Waehlby CellClump Splitter Waehlby CellClump Splitter Column Filter Joiner Image Converter Splitter Joiner Connected ComponentAnalysis Column Rename Zellzähler Math Formula Column Rename Labeling Arithmetic Labeling Filter Image Writer Labeling to RGB Img Segmentierung I Segmentierung II This workflow accompanies the manuscript of Akhtarand Stewart et. al. It is meant to perform an imagesegmentation of microscopic images with multicolorstainings to detect bacteria via fluorescent in situHybridization (FISH). The exemplary workflow usesimages recorded by a Zeiss LSM710 microscopewith a blue and a red fluorophor. If anothermicroscopic system and/or other fluorophores areused, the pipeline needs to be adjusted accordingly. Load imagesSplit clumps(Fluorophor I/ Column I)Split clumps(Fluorophor II/ Column II)Filter the columnsMerge data streamsConvert to Byte TypeSplit channelsMerge data streamsDetect connected componentsRename the columnsCount selected / gated cell populationCalculate fraction of doublelabeled cellsRename columnsCombine channelsFilter featuresSave result images as jpegConvert to RGBIndividual Segmentation AIndividual Segmentation B Image Reader Waehlby CellClump Splitter Waehlby CellClump Splitter Column Filter Joiner Image Converter Splitter Joiner Connected ComponentAnalysis Column Rename Zellzähler Math Formula Column Rename Labeling Arithmetic Labeling Filter Image Writer Labeling to RGB Img Segmentierung I Segmentierung II

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