Package: vpt
Vizgen Post-processing ToolThe Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.
VPT is a command line tool that emphasizes scalable, reproducible analysis, and can be run on a workstation, a cluster, or
be deployed in a cloud computing environment.FeaturesPerform cell segmentationReproduce standard Vizgen segmentation optionsPerform reproducible custom segmentationImport cell segmentation from other toolsSupports geojson and hdf5 formatsRegenerate single cell data with new segmentationCell by gene matrixCell spatial metadataImage intensity in each cellUpdate MERSCOPE Vizualizer file (vzg)Image format conversionConvert large tiff files to single or multi-channel Pyramidal OME-TIFF filesNextflow compatible, example pipeline providedInstallationInstall the tool through your choice ofpipDockerpoetryTo access in-utility help documentation run the process below in the installed environment.vpt--helpUsageVPT accepts two types of inputs to specify how to run segmentation:Command line parametersrelate to where to find the input data and are expected to vary with each experimentSegmentation algorithm .json file parametersdescribes a series of steps to perform on the input dataUsing the same segmentation algorithm on a series of experiments ensures that they are processed identically and reproducibly.In addition to the user guide, several working segmentation algorithm .json files are provided that can serve either as a
robust segmentation definition or as a template for a custom workflow.Quick start commands:run-segmentation    ​Top-level interface for vpt which invokes the segmentation functionality of the tool.​prepare-segmentation​Generates a segmentation specification json file to be used for cell segmentation tasks. ​run-segmentation-on-tile​Executes the segmentation algorithm on a specific tile of the mosaic images.​compile-tile-segmentation​Combines the per-tile segmentation outputs into a single, internally-consistent parquet file containing all of the
segmentation boundaries found in the experiment.​derive-entity-metadata​Uses the segmentation boundaries to calculate the geometric attributes of each Entity​partition-transcripts​Uses the segmentation boundaries to determine which Entity, if any, contains each detected transcript.​sum-signals​Uses the segmentation boundaries to find the intensity of each mosaic image in each Entity.​update-vzg​Updates an existing .vzg file with new segmentation boundaries and the corresponding expression matrix.​convert-geometry​Converts Entity boundaries produced by a different tool into a vpt compatible parquet file.​convert-to-ome​Transforms the large 16-bit mosaic tiff images produced by the MERSCOPE into a OME pyramidal tiff.​convert-to-rgb-ome​Converts up to three flat tiff images into rgb OME-tiff pyramidal images.​For more detail on commands and arguments, please see the user guide.DocumentationUser GuideFeedbackIf you encounter issues or bugs, let us know bysubmitting an issue!Please include:A quick issue summarySteps that caused it to occurThe exception generated by the code, if applicableSpecific lines of code, if indicated in the error messageIf you have any other feedback or issues, please reach out to your regional Vizgen field application scientist and CC: Vizgen
Tech Support attechsupport@vizgen.com.Please include VPT in your subject line along with the above information in the body.Contributing & Code of ConductWe welcome code contributions! Please refer to thecontribution guidebefore getting started.AuthorsVizgenLicenseCopyright 2022 Vizgen, Inc. All Rights ReservedLicensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License athttp://www.apache.org/licenses/LICENSE-2.0Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.