This guide walks you through the complete workflow for analyzing microscopy data with Cytely, from logging in to exploring your results on an interactive dashboard.

Getting Started

How do I access Cytely?

Simply log into your Cytely account at app.cytely.io. Once logged in, you'll be ready to upload and analyze your microscopy data.

Data Upload and Configuration

How do I upload my microscopy data?

Upload your microscopy files by dragging and dropping them directly into the Cytely interface. The platform supports various microscopy file formats and handles multi-channel images.

What configuration is required before analysis?

After uploading, you'll need to configure your dataset by:

  • Selecting the objective magnification used during imaging (e.g., 10x, 20x, 40x)
  • Assigning labels to different image channels (e.g., cell marker, prey marker, nucleus, etc.)

Analysis and Results

How do I start the analysis?

Once your dataset is configured, click the analyze button to start processing. Cytely's AI-powered algorithms will automatically detect and segment cells, measure features, and extract quantitative data from your images.

How will I know when my analysis is complete?

You'll receive an email notification when your analysis is complete. This allows you to work on other tasks while Cytely processes your data.

Data Exploration

What visualization tools are available?

Cytely provides an interactive dashboard with multiple visualization tools:

  • Overview maps showing the spatial distribution of your data
  • Thumbnails of detected objects for visual inspection of individual cells
  • Scatter plots for analyzing relationships between different measurements
  • Histograms showing the distribution of cellular features

How do I filter and analyze specific cell populations?

You can create "gates" on scatter plots to filter your data and focus on specific subsets of your sample. This allows you to isolate populations of interest based on any combination of measured parameters (size, intensity, morphology, etc.).

Can I provide feedback on the analysis quality?

Yes! Cytely includes a feedback system where you can rate the accuracy of the analysis. Your feedback helps improve the platform's AI algorithms and ensures better results for future analyses.