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https://github.com/biologytools/biolib

A GUI-less version of Bio .NET library for editing & annotating various microscopy image formats. Supports all bioformats supported images. Integrates with ImageJ, running ImageJ filters & macro functions.
https://github.com/biologytools/biolib

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A GUI-less version of Bio .NET library for editing & annotating various microscopy image formats. Supports all bioformats supported images. Integrates with ImageJ, running ImageJ filters & macro functions.

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README 

        
# BioLib

![Nuget](https://img.shields.io/nuget/dt/BioLib) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8127022.svg)](https://doi.org/10.5281/zenodo.8127022)



A GUI-less version of Bio .NET library for editing & annotating various microscopy image formats. Supports all bioformats supported images. Integrates with ImageJ, running ImageJ filters & macro functions. Supports Windows, Linux and Mac. Check out the [documentation.](https://biologytools.github.io/Documentation/BioLib/index.html)



## Usage

```

//First call BioImage.Initialize to 

//initialize the Bioformats library.

BioImage.Initialize();



//Once initialized you can open OME, ImageJ tiff files, and Bio Tiff files with:

BioImage b = BioImage.OpenFile("file");



//Or if you want to use specifically the OME image reader you can use BioImage.OpenOME

BioImage b = BioImage.OpenOME("file");



//If you are working with a pyramidal image you can open a portion of a tiled image with OpenOME.

//BioImage.OpenOME(string file, int serie, bool tab, bool addToImages, bool tile, int tilex, int tiley, int tileSizeX, int tileSizeY)



//You can specify whether to open in a newtab as well as whether to add the image to 

//the Images.images table. As well as specify whether to open as a tile with the specified 

//tile X,Y position & tile width & height.    

BioImage.OpenOME("file",0,false,false,true,0,0,600,600);

//This will open a portion of the image as a tile and won't add it to the Images table.



//Once you have opened a tiled image with BioImage.OpenOME you can call the 

//GetTile(BioImage b, ZCT coord, int serie, int tilex, int tiley, int tileSizeX, int tileSizeY) method

// to quickly get another tile from different portion of the image. For BioGTK & BioLib

Bitmap bm = BioImage.GetTile(b, new ZCT(0,0,0), 0, 100, 100, 600, 600);



//To get the current coordinate of the ImageView you can call GetCoordinate.

ZCT cord = v.GetCoordinate();

//or to set the current coordinate

v.SetCoordinate(new ZCT(1,1,1));



//To create a point as well as any other ROI type you can call the ROI create methods.

ROI p = ROI.CreatePoint(cord, 0, 0);

ROI rect = ROI.CreateRectangle(cord, 0, 0, 100, 100);



//Usage of Graphics class for 16 & 48 bit images as well as regular bit depth images

//is very similar to System.Graphics.

//We create a new Graphics object by passing the Bitmap for BioGTK & BioLib and BufferInfo for BioCore

Graphics g = Graphics.FromImage(b.Buffers[0]);



//Then we create a pen by passing a ColorS which represent a Color with, 

//a higher bit depth (unsigned short) rather than a byte.

g.pen = new Pen(new ColorS(ushort.MaxValue, ushort.MaxValue, ushort.MaxValue));



//Then we can call the familiar methods DrawLine, DrawPolygon, FillPolygon etc.

g.DrawLine(0,0,100,100);

//Finally we dispose the Graphics object.

g.Dispose();



//We can also save the resulting image given the ID of the image in the Images table.

//All images opened with BioImage.OpenFile or BioImage.OpenOME are added to the 

//Images.images table with the filename as an ID.

BioImage.SaveFile("file","path");



BioImage[] bms = new BioImage[]{BioImage.OpenFile("test.ome.tif")};

QuPath.Project qp = QuPath.Project.FromImages(bms, "test.qpproj");

QuPath.Project.SaveProject("myproj.qpproj", bms);



//To convert between different pixel formats we can call for example To24Bit.

b.To24Bit();

```