📖 PhenoCapture: Complete Feature Guide

Welcome to the comprehensive PhenoCapture Feature Guide. This guide provides an organized, menu-by-menu directory of all features, tools, and neural processing capabilities available within PhenoCapture, structured to strictly mirror the software’s native menu hierarchy.

📁 1. File Menu

Feature Name	Description
Open	Load standard raster images into the workspace.
Save As	Save the active workspace image with custom format settings.
Save Selection As Transparent Image	Export the selected region as an ARGB PNG with a transparent background.
Import Image from PDF	Render and import raster images directly from PDF documents.
Import Image from Photoshop File	Extract raster image data directly from Adobe Photoshop PSD files.
Import Image from Office File (docx, xlsx, pptx)	Extract embedded graphics from Word, Excel, and PowerPoint documents.
Export Grayscale to 3D STL	Convert 2D grayscale intensity maps into 3D STL surface meshes for 3D printing.
Print	Send the active canvas directly to physical printers or PDF drivers.
Exit	Close PhenoCapture and release all system and hardware resources.

📷 2. Device Menu

Feature Name	Description
Connect to HD Camera	Open the live webcam viewer with real-time AI background filtering.
Reconnect to HD Camera	Re-establish connection to USB camera hardware.
Record HD Video	Capture high-definition video feeds to MP4, WMV, or animated GIF formats.
Acquire Image from Scanner	Interface with TWAIN and WIA flatbed or document scanners.
Capture	Grab a single frame from the live video feed into the workspace.
Capture to	Transfer live snapshots directly to specified buffer boxes.
Video Source	Select connected video hardware inputs.
Video Format	Configure resolution, frame rate, and pixel encoding modes.
Disconnect	Safely release hardware video drivers and camera resources.

✂️ 3. Edit Menu

Feature Name	Description
Undo	Revert to the previous image state or selection snapshot.
Redo	Re-apply the next image state or selection snapshot in history.
Copy	Copy the active selection or canvas to the system clipboard.
Paste	Paste image data from the clipboard onto the canvas.
Unselect	Clear all active selection shapes and masks (Delete key).
Expand Selection	Dilate the selection boundary by a default pixel radius.
Expand Selection by Pixels	Dilate the selection boundary by a user-specified pixel value.
Shrink Selection	Erode the selection boundary by a default pixel radius.
Shrink Selection by Pixels	Erode the selection boundary by a user-specified pixel value.
Reverse Selection	Invert the current region selection mask across the canvas.
Create Selection From Binary Image	Convert a black-and-white mask image into an active interactive selection.
Add Binary Image to Selection	Merge new binary shapes into the existing selection mask.
Subtract Binary Image from Selection	Cut out binary shapes from the current selection mask.
Set Selection Box Size	Define exact numerical width and height dimensions for selection boxes.
Put to	Push the active selection or image to a Drag-drop Image Box buffer.
Get from	Retrieve image content from a Drag-drop Image Box buffer.
Clear Drag-drop Image Box	Reset and clear memory buffer slots in the Drag-drop Image Box.

🖼️ 4. Image Menu

Feature Name	Description
Flip	Mirror canvas orientation horizontally or vertically.
Crop	Trim the canvas strictly to the active selection boundary.
Rotate	Reorient the image by standard 90/180 degree steps or custom angles.
Resize	Rescale image pixel dimensions.
Resize Canvas	Expand or trim the canvas border padding without scaling image content.
Rotational Alignment by Straight Line	Level crooked photos by drawing a reference line along a known straight axis.
Box Averaging	Apply spatial box averaging smoothing filters across custom matrix sizes.
Gaussian Filter	Smooth high-frequency noise using Gaussian weighted convolution matrixes.
Smart Denoise	Suppress sensor noise while preserving sharp structural object edges.
Sharpen 3×3	Apply 3×3 kernel spatial edge sharpening.
Sharpen 5×5 High Quality	Apply high-precision 5×5 kernel spatial edge sharpening.
Advanced Sharpening	Fine-tune unsharp masking and local contrast enhancement parameters.
Correct Uneven Illumination	Equalize non-uniform lighting gradients across sample photos.
Rolling Ball Background Subtraction	Remove non-uniform background intensity variations for quantitative reads.
Overlay Image	Blend two images together using customizable transparency alpha levels.
Chroma Key	Isolate and knock out specific solid color backgrounds (green/blue screen).
Emboss	Apply 3D directional light relief texture effects.
Mosaic Filter	Pixelate selected regions or full images for privacy masking.
Dithering to Black and White Image	Convert grayscale images into 1-bit halftoned dithered representations.

🎨 5. Color Menu

Feature Name	Description
Auto Tone	Automatically balance overall color tonal distribution.
Auto Contrast	Automatically expand image dynamic range to full contrast limits.
Auto Equalize	Perform histogram equalization across image brightness channels.
Auto Gamma	Automatically adjust non-linear luminance response curves.
Auto White Balance	Correct color temperature and balance ambient light casts.
CIE L*a*b*	Adjust perceptual lightness and chromaticity a and b channels.
Multi-Band Color	Selectively manipulate specific hue bands across the spectrum.
Adaptive Constrast	Enhance local contrast adaptively across shadow and highlight regions.
Shadows/Highlights	Recover dark shadow details or clipped highlight areas locally.
Brightness/Contrast	Linear manual brightness and contrast level adjustments.
Hue/Saturation/Intensity	Adjust Hue, Saturation, and Intensity (HSI) color components.
Invert	Invert color channels to negative representations.
Gray Scaling	Convert color images into 8-bit monochromatic grayscale.
Gray to Color (Color Map)	Apply false-color thermal and rainbow gradients to grayscale intensity maps.
Split RGB to	Separate color images into distinct Red, Green, and Blue sub-images.
Gray From	Extract grayscale representations from individual RGB color channels.
Delete Channel	Remove specific Red, Green, or Blue channels from the color space.
Merge Channels	Combine separate grayscale channel images back into a composite RGB image.
Convert to rg Chromaticity	Normalize color space against light intensity changes for plant phenotyping.
Color Range Selection	Sample color ranges to generate active selection masks based on color similarity.
Change Color	Replace target color ranges with custom replacement colors across the canvas.

🧠 6. Neural-Processing Menu

Feature Name	Description
Smart Selection	Bounding-box interactive object segmentation powered by MobileSAM.
Auto Subject Selection (Portrait)	High-precision human subject extraction with hair alpha matting (MODNet).
Auto Subject Selection (General Object)	Universal object isolation for non-human subjects and products (U-2-Net).
1 Image Upscaling	Neural super-resolution upscaling to increase resolution while sharpening details.
2 Image Sharpening (Fast)	Fast AI neural edge sharpening and halo suppression.
3 Image Quality Restoration (Fastest)	High-speed lightweight AI neural image restoration.
4 Image Quality Restoration (Fast)	Balanced AI neural quality restoration for moderate noise and blur.
5 Image Quality Restoration (Slow)	Deep neural image quality restoration for enhanced fine details.
6 Image Quality Restoration (Slowest)	Maximum multi-pass deep learning restoration for severe blur and artifact removal.
Background Removal (Selfie)	Ultra-fast portrait background removal (MediaPipe).
Background Removal (Portrait)	Studio-grade human background removal with precise alpha matting boundaries.
Background Removal (General Object)	Universal AI background removal for products, animals, and general objects.
Inpainting	Context-aware AI object removal and flaw healing.
Depth Estimation	Predict 3D surface depth maps directly from single 2D photographs.
Document Unwarp	Flatten, deskew, and unwarp curved book page scans.
OCR Text Extraction	Extract editable text from document images while retaining formatting.
Binarization and Segmentation	Neural biological cell binarization and segmentation.
Custom Binarization	Execute dynamically loaded user-trained ONNX binarization neural networks.
Custom Binarization Trainer	Train custom ONNX segmentation models using paired training image datasets.
Image Classification	Automated neural image recognition and classification.

⚙️ 7. Processing Menu

Feature Name	Description
Fill Region	Flood-fill the selected region with a solid color.
Text Annotation	Add customizable text labels, fonts, and annotations directly onto the canvas.
Draw Selection Border Line	Render visible outline strokes along active selection boundaries.
Manual Binarization	Convert grayscale images to 1-bit black/white using manual threshold sliders.
Adaptive Binarization	Apply local adaptive neighborhood thresholding to handle uneven lighting.
Multi-Step Thresholding	Segment images into discrete intensity steps or multi-level threshold bands.
Super-Pixel Segmentation	Group perceptually similar neighboring pixels into atomic super-pixel clusters.
Change Non-black Pixels to White	Convert all non-black background areas into pure white.
Erode	Apply grayscale or binary structural kernel erosion.
Dilate	Apply grayscale or binary structural kernel dilation.
Canny Edge Detection	Extract object boundaries using multi-stage Canny gradient operators.
Edge Detection	Extract spatial edges using directional Sobel gradient matrices.
Edge Detection – Homogenity	Detect edges based on local pixel neighborhood homogeneity variance.
Average Image	Compute mean pixel intensity across multiple loaded images.
Differential Image	Calculate pixel-by-pixel differential difference maps between two images.
Fast Fourier Transform (FFT) Magnitude	Convert spatial images into frequency domain magnitude spectra to analyze periodic patterns.

⬛ 8. Binary Menu

Feature Name	Description
Outline	Extract 1-pixel outer perimeter contours from binary shapes.
Skeletonize	Reduce binary structures to topological medial-axis centerline skeletons.
Skeletonize – Extended	Extended thinning morphological algorithm for complex interconnected networks.
Region Coloring	Assign distinct pseudo-colors to isolated disconnected binary particles.
Erode	Erode binary foreground region boundaries.
Dilate	Expand binary foreground region boundaries.
Erode Outline	Erode outer border lines of binary shapes.
Dilate Outline	Expand outer border lines of binary shapes.
Hide Outlines	Suppress and hide binary outline overlays from canvas display.
Watershed Segmentation	Separate touching circular biological particles using distance-transform watershed lines.
Hough Transform for Circles	Detect circular shapes and boundaries mathematically in binary images.
Hough Transform for Lines	Detect straight lines and linear structural vectors mathematically.
Binary Operation	Perform logical Boolean operations (AND, OR, XOR, NOT) between binary masks.
Boundary Detection in Region	Extract perimeter boundaries within selected regions of interest.
Remove Black Dots	Filter small pinhole background noise specks below area thresholds.
Remove White Dots	Filter small foreground noise specks below area thresholds.

📐 9. Analysis Menu

Feature Name	Description
Line profile	Plot pixel intensity distribution curves along a user-drawn line cross-section.
Histogram	Display pixel brightness and channel color distribution charts.
Region Extraction	Automatically crop and save disconnected particle regions into separate image files.
Particle Color Analysis	Quantify area, perimeter, shape factors, and color values for all detected particles.
Color Quantification	Measure percentage composition of specific color ranges across selected regions.
Pixel Counter	Count total foreground versus background pixels in active selection areas.
Average Color Value	Compute mean Red, Green, and Blue color values across active regions.
Multiple Cell Analysis	Batch analyze multi-well assay plates or grid cell arrays simultaneously.
Length Measurement	Measure spatial distances using calibrated physical unit scale markers (μm, mm, cm).
Custom Coordinate	Establish custom reference origin points and coordinate axes.
Point Location Recorder	Interactively log (X, Y) coordinates by clicking features, exporting results to CSV.
Edge Location Measurement	Measure exact pixel distance spacing between parallel structural edges.

🛠️ 10. Tool Menu

Feature Name	Description
Script Runner	Write, debug, and execute custom automation scripts in Python, JavaScript, or VBScript.
Batch Processing	Build multi-step action workflows to automatically process hundreds of images and export CSV data.
Time-lapse Image Capture	Schedule automated periodic image acquisition from cameras or screen regions.
Automatic Image Downloader	Automatically scrape and download image collections from web sources.
Online Live View Web Service	Stream live camera feeds directly to local or web browsers.
FTP Image Upload Service	Automatically upload captured time-lapse images to remote FTP servers.
Remote Webcam Server	Broadcast live camera video feeds over local IP networks.
Remote Webcam Client	Receive and process live camera video streams over local IP networks.
Quick Animation	Merge 2 to 5 still frames into looping animated GIFs with smart cropping.
Create Video or Animated Gif File from Images	Encode large image sequences into MP4, WMV, or Animated GIF files.
Batch Text Writer	Stamp custom text, watermarks, or timestamps across entire folders of photos.
Extract Frames from Video File	Navigate video files frame-by-frame to extract high-resolution still photos or image sequences.
Image Augmenter	Generate synthetic augmented image datasets (rotations, flips, noise) for AI training.

👁️ 11. View Menu

Feature Name	Description
Zoom In	Increase canvas magnification level.
Zoom Out	Decrease canvas magnification level.
Zoom 100%	Reset canvas display magnification to 1:1 native pixel ratio.
Zoom to Fit	Fit the active image dimensions strictly within the workspace window.
Multiple ROIs	Save and manage multiple distinct Regions of Interest across the image canvas.
File Manager	Open the integrated thumbnail file browser to navigate image folders.
Drag Drop Image Box	Dockable side panel for temporary image buffer slots.
Drag Drop Image File Box	Dockable side panel for queuing image file paths for batch jobs.
Toolbox	Floating toolbox window for quick one-click access to core image processing tools.
Selection Tool (Magnetic Snap & Auto-Routing)	Toggle interactive selection tools with magnetic edge snapping and auto-routing.
Reset Window Layout	Restore default panel docking positions and UI window dimensions.
DPI Settings	Configure high-DPI display scaling overrides for crisp rendering.

❓ 12. Help Menu

Feature Name	Description
About	View PhenoCapture version build, copyright, and registration details.
Visit our website	Open the official PhenoCapture website in your default web browser.
View Third-Party Libraries and Models	View credit list of open-source libraries, ONNX models, and dependencies.
Open Third-Party License Folder	Open the local directory containing full text licenses for embedded third-party components.
Activate Product	Enter license key information to unlock PhenoCapture Pro commercial capabilities.
Download MS Visual C++ Runtime Redistributables	Direct download link for required Microsoft Visual C++ runtime runtime libraries.