Vizgen Post-processing Tool for Cell segmentation
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.
Alternate Cell Segmentation
Experiment with alternative segmentation options (Methods, parameters, reprocess, or image channels)
Deep Learning Models
Use custom trained Deep-learning models on your dataset (Cellpose)
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.
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.
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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.