SciTIF 0.1.2

SciTIF is a .NET Standard library for working with scientific imaging data. Many libraries that read TIF files struggle to interpret 16-bit, 32-bit, and 8-bit indexed color TIFF files used for scientific imaging. If you've ever tried to open a scientific TIF file and been presented with an all-black or all-white image, you've experienced this problem too! SciTIF supports 5D TIF files with separate axes for X, Y, C (channel), Z (slice), and T (frame).

Quickstart

// Open a 16-bit TIFF with pixel values that exceed 255
var tif = new TifFile("input.tif");

// Get a channel of interest from the 5D TIFF file
Image slice = tif.GetImage(frame: 0, slice: 0, channel: 0);

// Analyze or manipulate images by iterating the flat pixel value array
double[] allValues = slice.Values;

// ...or manipulate individual pixels as desired
double pxValue = slice.GetPixel(13, 42);
slice.SetPixel(13, 42, 123);

// Scale the pixel values down to 0-255 and save as a PNG file
slice.AutoScale(max: 255);
slice.Save("output.png");

3D Image Projection

This examples shows how to create a maximum-intensity projection along the Z axis of a 5D TIF image. This can be used to create all-in-focus maximum projection of a collection of single optical sections.

TifFile tif = new("16bit stack.tif");
ImageStack stack = tif.GetImageStack();
Image projection = stack.ProjectMax();
projection.AutoScale(max: 255);
projection.Save("projection.png");

Multi-Channel Merge

// load a 3-channel TIF and merge channels as an RGB image

string path = System.IO.Path.Combine(SampleData.Tif3Channel);
TifFile tif = new(path);

Image red = tif.GetImage(channel: 0);
Image green = tif.GetImage(channel: 1);
Image blue = tif.GetImage(channel: 2);

ImageRGB rgb = new(red, green, blue);
rgb.Save("merge.png");

Notes

• Warning: SciTIF is still version 0 so its API may change as it continues to evolve.

• Note: RGB images are automatically split into 5D TIF files containing 4 channels: Red, Green, Blue, and Alpha.