clij-opencl-kernels

This repository contains a collection of OpenCL kernels for image processing. The CLIJ is build on top of it allowing ImageJ / Fiji users in doing GPU-accelerated image processing without the need for learning OpenCL.

If you use it, please cite it:

Robert Haase, Loic Alain Royer, Peter Steinbach, Deborah Schmidt, Alexandr Dibrov, Uwe Schmidt, Martin Weigert, Nicola Maghelli, Pavel Tomancak, Florian Jug, Eugene W Myers. CLIJ: GPU-accelerated image processing for everyone. Nat Methods (2019) doi:10.1038/s41592-019-0650-1

Why a custom OpenCL-dialect?

OpenCL offers several pixel types, such as uint8, unit16 and float. Theoretically, one has to write OpenCL-kernels specifically for given input- and output-images, such as a kernel for adding images of type float resulting in a float image and a kernel for adding image of type uint8 resulting in an image of type float. Furthermore, OpenCL defines images and buffers. However, as both are arrays of pixel intensities in memory, we wanted to access them in a unified way. As this would result in a ridiculous large number of individual kernel implementations, we used a dialect where placeholders such as IMAGE_src_PIXEL_TYPE represent the pixel type of the output image.

List of placeholders

The following list of placeholders are used at the moment. The name imagename must contain src or dst to differentiate readonly and writeonly images.

Place holder	Replacement during runtime
CONVERT_imagename_PIXEL_TYPE	clij_convert_char_sat clij_convert_uchar_sat clij_convert_short_sat clij_convert_ushort_sat clij_convert_int_sat clij_convert_uint_sat clij_convert_float_sat	Convert any number to a given type.
IMAGE_imagename_TYPE	__read_only image3d_t __read_only image2d_t __write_only image2d_t __write_only image3d_t __global char* __global uchar* __global short* __global ushort* __global float*	Two dimensional input image type definition.
IMAGE_imagename_PIXEL_TYPE	char uchar short ushort float	Pixel type definition
GET_IMAGE_DEPTH(imagename)	constant number	Image size in Z
GET_IMAGE_HEIGHT(imagename)	constant number	Image size in Y
GET_IMAGE_WIDTH(imagename)	constant number	Image size in X
POS_imagename_TYPE	int2 int4	Type of coordinate
POS_imagename_INSTANCE(pos0,pos1,pos2,pos3)	int2(pos0, pos1) int4(pos0,pos1,pos2,pos3)	instantiate variable of coordinate
READ_imagename_IMAGE	read_imageui (2d) read_imagef (2d) read_buffer2dc read_buffer2duc read_buffer2di read_buffer2dui read_buffer2df read_imageui (3d) read_imagef (3d) read_buffer3dc read_buffer3duc read_buffer3di read_buffer3dui read_buffer3df	Read pixel intensity from a given position
WRITE_imagename_IMAGE	write_imageui (2d) write_imagef (2d) write_buffer2dc write_buffer2duc write_buffer2di write_buffer2dui write_buffer2df write_imageui (3d) write_imagef (3d) write_buffer3dc write_buffer3duc write_buffer3di write_buffer3dui write_buffer3df	Write pixel intensity to a given position

Known issues

• Image dimensionality is limited to three dimensions.

Acknowledgements

We acknowledge support by the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy (EXC2068) Cluster of Excellence Physics of Life of TU Dresden. This project has been made possible in part by grant number 2021-237734 (GPU-accelerating Fiji and friends using distributed CLIJ, NEUBIAS-style, EOSS4) from the Chan Zuckerberg Initiative DAF, an advised fund of the Silicon Valley Community Foundation.