Multiplex IMC image before running this APP.
#10184
Nuclei Detection, AI (IMC)
Automatically segment cells in your IMC (imaging mass cytometry) images to perform multiplexed nuclear profiling. All you need are images acquired from your Hyperion XTi Imaging system. This APP runs on the DNA channels, ensuring that no matter how noisy the image is, nuclei are segmented accurately.
After analysis is complete, you may explore your results with the Phenoplex™ Guided Workflow or the Data Exploration and QC tool (available on Discovery and Phenoplex™).
As with all of our Quickstart APPs and custom-build APPs, your image analysis can be scaled by queueing APPs to run in the background on an unlimited number of images and cores—this is possible with the “batch analysis” feature available on both Discovery and Phenoplex™.
Working with multimodal data sets or TMAs? No problem. Run this APP after using the Tissuealign™ feature to align your images at the cellular level, or the Tissuearray™ feature to de-array your tissue cores.
After this APP has been run, nuclei are clearly segmented.
An IMC image with only the two DNA channels (stained with iridium) selected.
Nuclei are segmented clearly based on the DNA channels, as seen in the post-processed image.
Details
Quantitative Output variables
- Total number of nuclei
- Biomarker intensity for each nucleus
Workflow
After loading your IMC image, follow these steps.
Step 1: Open the “10184 – Nuclei Detection, AI (IMC)” APP.
Step 2: Select a region of interest to limit analysis to one area, or skip to next step.
Step 3: Click “Run APP”. A dialogue box will appear where you must set the input channel to match the iridium (DNA1 and DNA2) channels. Once saved, perform batch analysis to queue this APP and keep working on other images.
