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Created with Raphaël 2.2.03Feb226Jan259822Dec21201913Nov10763231Oct30272625222019181716141312111098529Sep2827262513127654131Aug302928242322Moved zmask generation into RoiSet methodPass RoiSet object to products, much easierStable testsBrought some patch generation / export functionality into RoiSetAll tests now interface with RoiSet object instead directlyTest that calls RoiSet directlyStandardized RoiSet constructor works on object id mapsz-stack tests passSome test coverage, those that are failing are because of issues propagating nested parameters to pydantic modelsRepaired import statementRemoved trivial diffs from chaeo_extensionAdapted folder structure from masterAdapted folder structure from masterTests passThis seems to be an orphaned fragment of something elseChange to folder structure on masterTuning parameters using boundary pixel classifierMade a workaround for passing all channels to pixel classifier; stable export script using this from multiposition CZIsManually made correction that is already implemented on masterAllow YXZ from TIF filesScript to export patch stacks from non-PA TREC dataDebugging loop on multichannel CZIImplemented utility functions to export subblock and XML data from CZI files, as well as to return a single position's accessor from a multiposition fileDefault mip=False in ilastik workflow APICorrect reference error in ilastik configurationoptionally make MIP when extracting single channel from accessorReorganzed ImageJ example to exist outside this codebaseChange default path for session dataMade ImageJ example script a bit more user-friendlyAdded ImageJ exampleMerge branch 'master' of git.embl.de:rhodes/model_serverAdditional installation instructionAdditional installation instructionAdditional installation instructionAdded retry mechanism to status confirmation, to address suspect timeout problemRebuilt dependency filesUser path variables in prompt instructionsUpdated run_server command with relative path to user profile for mamba promptUpdated run_server command with relative path to user profile for mamba promptChanged ImageJ examples