Vizgen Post-processing Tool Cellpose Plugin

The 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.

Cellpose

The Cellpose plugin for VPT is an interface to Cellpose 1.0.2:

Stringer, C., Wang, T., Michaelos, M., & Pachitariu, M. (2021). Cellpose: a generalist algorithm for cellular segmentation. Nature methods, 18(1), 100-106.

Addtional information about Cellpose can be found at https://www.cellpose.org/

Documentation

User Guide

Feedback

If you encounter issues or bugs, let us know by submitting an issue! Please include:

• A quick issue summary
• Steps that caused it to occur
• The exception generated by the code, if applicable
• Specific lines of code, if indicated in the error message

If you have any other feedback or issues, please reach out to your regional Vizgen field application scientist and CC: Vizgen Tech Support at techsupport@vizgen.com.

Please include VPT in your subject line along with the above information in the body.

Contributing & Code of Conduct

We welcome code contributions! Please refer to the contribution guide before getting started.

Authors

• Vizgen

License

Copyright 2022 Vizgen, Inc. All Rights Reserved

Licensed 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 at

   http://www.apache.org/licenses/LICENSE-2.0

Unless 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.