BioGTK 2.3.0

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 Mac see installation instructions. For Discussion check out the new Discord Server. https://discord.gg/NpREVubS

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# functions.

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

• Use AForge filters by opening filters tool window and right click to apply. Currently supports only some AForge filters as many of them do not support 16bit and 48bit images. Convert to 8bit image to make use of more filters. Applyed filters can be easily recorded and used in scripts. Bio impliments some filters like crop for 16 & 48 bit images.

• Star this project on Github to help spread the word about Bio!

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.
• If you experience a crash when opening a new TabsView the fix is runnning the application via terminal, by opening the package contents by right click and then double clicking BioGTKApp. This will open the application via terminal and show any warnings or errors.

Sample Tool Script

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";
}
}```