BioGTK 2.5.0

BioGTK

A .NET application & library for editing & annotating various microscopy image formats. Supports all bioformats supported images. Integrates with ImageJ, running ImageJ filters & macro functions.Check out the new wiki for library usage. or check out the documentation. Supports Windows, Linux and Mac. For Windows & Mac see installation instructions. For Discussion check out the new Discord Server. https://discord.gg/tdeyc6fgpv

Features

• C# scripting with sample tool-script and other sample scripts in "/Scripts/" folder. See samples

• Supports running ImageJ macro commands on images open in Bio. Console to run ImageJ macro commands and Bio C# scripts.

• Supports Pyramidal images with multiple resolutions. Like whole slide images.

• Multiple view modes like Emission, and Filtered. ROI's shown for each channel can be configured in ROI Manager.

• Supports drawing shapes & colors onto 16 bit & 48 bit images, unlike System.Drawing.Graphics.

• Convenient viewing of image stacks with scroll wheel moving Z-plane and mouse side buttons scrolling C-planes.

• Editing & saving ROI's in images to OME format image stacks.

• Copy & Paste to quickly annotate images and name them easily by right click.

• Select multiple points by holding down control key, and move them by holding down control key.

• Exporting ROI's from each OME image in a folder of images to CSV.

• Easy freeform annotation with magic select tool which selects based on blob detection.

• Whole slide image supported formats: .ndpi, .czi, .ome.tif.

Dependencies

• BioFormats.Net
• IKVM
• AForge
• LibTiff.Net
• Cs-script
• ImageJ (Only needed when running ImageJ macro commands)

Licenses

• BioGTK GPL3
• AForge LGPL
• BioFormats.Net GPL3
• IKVM
• LibTiff.Net BSD
• Cs-script MIT

Scripting

• Save scripts into "StartupPath/Scripts" with ".cs" ending.
• Open script editor and recorder from menu.
• Scripts saved in Scripts folder will be loaded into script runner.
• Use Script recorder to record program function calls and script runner to turn recorder text into working scripts. (See sample scripts

Mac Installation

• Install Mac package manager homebrew.
• From brew install GTK3.
• Download the BioGTK application for either OSX-x64 or OSX-Arm from releases.
• Make the file executable by opening terminal in the extracted folder and running "chmod 755 BioGTKApp"

Windows Installation

• Install package manager MSYS2. to install package GTK3. (Required for GTK Apps.)
• Download the BioGTK Windows installer from releases.

Sample Tool Script

//css_reference BioGTK.dll; 
using System; 
using BioGTK;
using System.Threading;
using AForge;
public class Loader {

//Point ROI Tool Example
public string Load()
{
	int ind = 1;
	do
	{
		BioGTK.Scripting.State s = BioGTK.Scripting.GetState();
		if (s != null)
		{
			if (!s.processed)
			{
				if (s.type == BioGTK.Scripting.Event.Down && s.buts == 1)
				{
					ZCT cord = BioGTK.App.viewer.GetCoordinate();
					BioGTK.Scripting.LogLine(cord.ToString() + " Coordinate");
					BioGTK.ROI an = BioGTK.ROI.CreatePoint(cord, s.p.X, s.p.Y);
					BioGTK.ImageView.SelectedImage.Annotations.Add(an);
					BioGTK.Scripting.LogLine(cord.ToString() + " Coordinate");
					an.Text = "Point" + ind;
					ind++;
					BioGTK.Scripting.LogLine(s.ToString() + " Point");
					//ImageView.viewer.UpdateOverlay();
				}
				else
				if (s.type == BioGTK.Scripting.Event.Up)
				{
					BioGTK.Scripting.LogLine(s.ToString());
				}
				else
				if (s.type == BioGTK.Scripting.Event.Move)
				{
					BioGTK.Scripting.LogLine(s.ToString());
				}
				s.processed = true;
			}
		}
		if(BioGTK.Scripting.Exit("points.cs"))
		{	
			return "OK";
		}
	} while (true);
	return "OK";
}
}