🌿 Rootify User Guide

Welcome to Rootify, an AI-powered Streamlit app designed to support plant scientists and researchers in analyzing root structures through image processing. This guide explains how to use the app for:

• 🧠 Root mask generation

• 📍 Root tip detection

• 📏 Root length measurement

🚀 Getting Started

Step 1: Open the App

Launch the Streamlit app in your browser. You'll be greeted with the Rootify welcome screen and feature overview.

🗂️ Choose Input Mode

You have two input options:

• Single Image – Analyze one image at a time.

• Folder of Images – Analyze multiple images in a batch.

Select your preferred mode using the radio buttons.

🔧 Set Conversion Factor

Set the Pixels per Millimeter (PPM) value using the number input field.

This is used to convert pixel measurements into real-world lengths (mm).

Default: 1.0

📤 Upload Your Image(s)

• If in Single Image mode: click to upload one .jpg, .jpeg, or .png file.

• If in Folder of Images mode: upload multiple image files at once.

Once uploaded:

• A preview of each image will appear.

• The app will automatically start processing each image.

Accepted Image Requirements

Please ensure that the uploaded images meet the following criteria:

• The image contains a Petri dish with clearly visible edges, allowing clear separation from the background.

• The Petri dish includes no more than five plants.

• All plants must be Arabidopsis thaliana.

• The roots must not be overlapping or crossing each other.

🧠 What Happens During Processing?

For each uploaded image, Rootify:

1. Generates a root mask using a deep learning model.

2. Extracts root tip coordinates.

3. Calculates root lengths (based on the given pixel-to-mm conversion).

You'll see:

• 🔬 Loading spinner during processing.

• ✅ Success messages when steps complete.

📊 View Results

For each image:

• 🖼️ Mask: See and download the predicted root mask.

• 📍 Tip Coordinates: Listed with labels (e.g., Tip 1: [x, y]).

• 📏 Root Lengths: Displayed in millimeters (e.g., Root 1: 25 mm).

📥 Export Results

At the bottom of the app, you can download:

1. All Predicted Masks (ZIP)

   • Includes individual *_mask.png files for each uploaded image.

2. CSV Summary File

   • Contains:

     • image name

     • root_lengths_mm: Comma-separated lengths

     • tip_coordinates: Semicolon-separated coordinate lists

🔄 Reset Application

Click the 🔄 Reset Application button at any time to:

• Clear uploaded images

• Reset session state

• Restart from the input selection

⚠️ Error Handling

• ❌ Invalid image files are rejected with a clear message.

• 🛠️ Unexpected model response formats trigger a warning.

• 📉 No roots detected will be noted per root index.

🧪 Technical Requirements

• Accepted file types: .jpg, .jpeg, .png

• Backend dependencies: Custom APIs exposed in deployment.api.main:

  • predict_mask_api

  • extract_root_tips

  • calculate_root_lengths

💬 Support

For technical issues or questions about integrating your own models, reach out to the development team.