Vizgen Post-processing Tool for Cell segmentation
MERFISH technology identifies the location of transcripts across tissue sections with submicron precision. However, only localizing transcripts doesn’t provide a single-cell view of tissues. The Vizgen Post-processing Tool (VPT) uses cell segmentation methods to draw cell boundaries and generates single-cell output by combining the results with MERFISH data. With VPT, users can change methods of cell segmentation to better fit the data for improved single-cell analysis.
Download a Sample Dataset
Dive into the intricate world of cell segmentation with our Vizgen Post-processing Tool (vpt). For users with knowledge of bioinformatics processes, this tool will assist in reanalyzing your existing MERSCOPE® Platform datasets or conducting additional segmentation from your own custom plugin. To get started, utilize the sample data set below and follow along with a common use case.
Dataset Walk Through
Using the sample dataset, follow along to understand how to segment a dataset that is saved to the local harddrive. This will take you through the process of getting familiar with the tool and running a common segmentation use case.
Alternative Cell Segmentation
Experiment with methods, parameters, and image channels (Watershed, Cellpose2, Cellpose-SAM, InstanSeg)
Deep Learning Models
Use custom-trained Deep-learning models on your dataset
Plugins
Develop fully custom methods with the plugin architecture
Getting started with VPT
VPT runs on data generated by the MERSCOPE® Platform and conducts cell segmentation and other functions. Deployment is intended to be on a Linux server or a high-computing cluster.
Users trying to image smaller datasets and items can utilize a workstation.
System requirements
VPT can be run on a minimum system* with the following criteria:
- Processor: 11th Generation Intel® Core™ i7 Processor or equivalent
- RAM: 16 GB or greater
- SSD Capacity: Based on data size
For optimal performance, improvements to RAM size and additional CPU processing cores can reduce run time and system strain. VPT can be run on a system with the above capability, but may result in suboptimal and increased processing time, especially for large datasets.
*A system with an NVIDIA GPU with at least 8GB of memory is strongly recommended when using the Cellpose-SAM plugin. Cellpose-SAM can run on a CPU, but performance will be significantly slower.
Sign Up to Stay Informed of Updates to the VPT!
Interested in starting a MERFISH spatial profiling project at Vizgen? Fill out the form below and a member of the Lab Services team will get in touch within 2-3 business days to set up a project consultation call.