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EVAnalyzer Docs

First Steps

This guide walks you through the essential workflow: open a set of images, configure object classes and pipelines, run the analysis, and inspect the results.

1. Open EVAnalyzer

Start EVAnalyzer as described in Installation. The application opens showing the project configuration panel on the left and an empty image viewport on the right.

2. Set Up Your Project

The left-hand navigation panel contains four tabs that must be configured in order: Project → Images → Classification → Pipelines.

Project tab

Enter basic experiment metadata and select the image directory:

  • Image directory — the folder containing your microscopy images. EVAnalyzer scans this folder recursively and lists all supported files.
  • Job name — a label for this analysis run (auto-generated if left blank).
  • Grouping — leave as Ungrouped for a simple run, or choose Filename / Foldername to group images into wells for plate-based experiments.

Images tab

Once the directory is set, EVAnalyzer lists all found image files. Click an image to preview it and inspect its metadata (channels, pixel sizes, Z/T dimensions).

Classification tab

Before building pipelines, define the object classes you want to detect — for example, dapi@nucleus, cy5@spot, cy7@spot.

  • Click the + button to add a class.
  • Assign a name and a display colour.
  • Optionally choose which metrics to show by default in the results view.

Pipelines tab

Pipelines extract objects from image channels. Click New pipeline (or select a preset from the + dropdown) and then open the pipeline editor by clicking the pipeline name.

A minimal spot-detection pipeline looks like:

  1. Rolling Ball — remove uneven background
  2. Gaussian Blur — reduce noise
  3. Threshold — convert greyscale to binary
  4. Connected Components — label each foreground region
  5. Watershed — split touching objects
  6. Extract ROIs — assign the segmentation class
  7. Classify ROIs — filter by size/circularity and assign an object class

The live preview on the right updates immediately as you change parameters.

3. Run the Analysis

Click the Play button in the toolbar. A progress dialog appears. When complete, click Open results folder to locate the output files, or click Close to view results within the application.

Results are saved to:

<image_directory>/evanalyzer/<job_name>/results.evadb

4. View Results

Click the results icon in the toolbar (or use File → Open Results) to open the results viewer.

  • Plate view — aggregated statistics per well (only when grouping is configured).
  • Image view — per-image statistics table.
  • Detail view — density map and per-object interactive mode; click an object row to highlight it in the image.

See the Results guide for full details.

Next Steps

  • Read Project Setup for all project options including Z-stack and T-stack handling.
  • Read Pipelines for a detailed explanation of every pipeline option.
  • Browse the Commands reference to learn what each pipeline step does.
  • Follow a Tutorial for a complete worked example.