subvoxel-resolving-algorithm

Executable program and example data for Subvoxel-resolving algorithm.

Requirements:

• Windows 7 or later
• NVIDIA CUDA Toolkit 7.5 and 8.0

Install

Download and unpack the repository.

Usage

1. Unpack the example data /subvoxel-resolving-algorithm/test data/raw.zip in place.

2. Open profile.ini, set “INPUT0” to the example data path. Note:

   • The images should be sequential tif images with the same prefix pattern.
   • The width and height of each image should be the same and integer multiples of 128 px.

3. Edit and save commom.ini. The options are as follow:

   • Output_dir : directory to save the results.

   • PSFfile: your PSF file path.

   • X_src, Y_src, Z_src : Width, height and sequence length of the input (in pixels).

   • XZ_angle, YZ_angle: the off-axial angle (degree).

   • Z_step : light-sheet scanning step size (in um).

   • X_res, Y_res : lateral voxel size of the input (in um, determined by the magnification and the camera sensor patch size).

   • Z_res : axial voxel size of the input (in um, usually is half of the light-sheet thickness).

   • X_factor, Y_factor, Z_factor : resolution enhancement factors.

   • PSF_X, PSF_Y : size of the PSF (in pixels).

4. Double click run.bat. The "Deconvxx.tif" under the output diretory is the final result.