{"Id":"fb649d58-1eb1-4f6c-864f-48c22bac356a","CanonicalId":"","Url":"https://github.com/BodenmillerGroup/ImcSegmentationPipeline","Name":"ImcSegmentationPipeline","Description":"A flexible image segmentation pipeline for heterogneous multiplexed tissue images based on pixel classification. The pipeline is based on CellProfiler (http://cellprofiler.org/, v1.3.5) for segmentation and Ilastik (http://ilastik.org/) for for pixel classification. It is streamlined by using the specially developped imctools python package (https://github.com/BodenmillerGroup/imctools) package as well as custom CellProfiler modules (https://github.com/BodenmillerGroup/ImcPluginsCP).","ResourceType":"CodePipelineTechnology","ParentResourceType":"Technology","DefiningManuscriptId":"PMID29605184","Publications":[],"Contributors":[{"Role":{"CanonicalId":"hirn-cv-ResourceRole-producer","Url":"resources.hirnetwork.org/api/v1/CV/","Name":"Producer","OntologyId":"HIRN"},"HirnUserId":"bernd_bodenmiller@hirnetwork.org","FirstName":"Bernd","LastName":"Bodenmiller","EmailAddress":"bernd.bodenmiller@imls.uzh.ch","Organization":"University of Zurich","Consortia":["CBDS"]}],"Vendor":{"id":null,"Name":null,"Url":null},"VendorResourceName":null,"VendorResourceUrl":null,"VendorCatNumber":null,"VendorLotNumber":null,"DateCreated":"2019-04-26T01:22:19.5718812+00:00","DateModified":"2022-07-01T03:35:15.7128784+00:00","VersionId":"1","ModelVersion":"4.0","TechnologyData":{"Dependencies":[],"AssayTechnologyData":{"BioSampleType":[],"CellsTestedWith":[],"AssayTarget":{"CanonicalId":null,"Url":null,"Name":null,"OntologyId":null},"AssayCategory":{"CanonicalId":null,"Url":null,"Name":null,"OntologyId":null},"TechnologyType":{"CanonicalId":null,"Url":null,"Name":null,"OntologyId":null},"TechnologyPlatform":null,"CompatibleTools":[]},"DeviceEquipmentTechnologyData":{"CompatibleTools":[],"CellsTestedWith":[],"Placeholder":"Test"},"ServiceTechnologyData":{"CellsTestedWith":[],"Placeholder":"test"},"CodePipelineTechnologyData":{"Placeholder":"Test"}}}