ODT_FieldTomogramGUI

Overview

ODT_FieldTomogramGUI is a MATLAB-based graphical user interface (GUI) designed for field retrieval and 3D tomogram reconstruction in optical diffraction tomography (ODT). It enables users to visualize and reconstruct refractive index distributions from off-axis holographic measurements with minimal programming effort.

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System Requirements

Hardware

• A computer equipped with an NVIDIA GPU is recommended to enable GPU-accelerated tomogram reconstruction.
• Minimum requirement: GPU with 4 GB of memory.

Software

• MATLAB R2018a or later
• Required toolboxes:
  • Parallel Computing Toolbox
  • Image Processing Toolbox

Installation Guide

1. Download and place all files (Field_Tomogram_Reconstruction.fig, Field_Tomogram_Reconstruction.m, and auxiliary scripts) into the same directory.
2. In MATLAB, set the path to this directory using:

   addpath('path_to_your_folder');

3. Launch the GUI by running the main .m script (e.g., Field_Tomogram_Reconstruction.m).

Input Data

The software requires at least two .mat files located in the same folder:

• sample*.mat: Off-axis holograms of samples (use consistent sample naming).
• bg*.mat: Background (empty field-of-view) holograms.

Each .mat file should include the following variables required for field retrieval and tomogram reconstruction:

• res: Pixel resolution (in µm). This is the image-plane resolution, calculated as camera pixel size divided by total magnification.
• NA: Numerical aperture of the detection objective lens.
• lambda: Illumination wavelength (in µm).
• tomogMap: A 3D array of raw holograms (x, y, θ) from 150 illumination angles. The hologram corresponding to normal illumination should be at index 49.

A demo dataset is available for download at:https://doi.org/10.6084/m9.figshare.28988165.v1

The sample contains a nucleus in a Xenopus egg extract, as presented in the following study:

Biswas, A. et al. (2023). Conserved nucleocytoplasmic density homeostasis drives cellular organization across eukaryotes. bioRxiv. https://doi.org/10.1101/2023.09.05.556409

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How to Use

The workflow consists of three steps:

1. Sample Selection (Gray Box)

1. Click "Browse" to select the folder containing the sample and background .mat files.
2. The surrounding medium’s refractive index is preset to 1.337 by default. Update this value if using a different medium.
3. If multiple background files are available, you can select one using the "Background #" field.

2. Field Retrieval (Red Box)

1. Choose the Analysis Option to retrieve the field from either a single hologram or all sample holograms.
2. Click "Retrieval" to begin. The progress is displayed in real time.
3. Field retrieval for a single sample typically takes 1–2 minutes, depending on your system’s specifications.
4. Once completed:
   • The phase delay map at normal incidence is shown.
   • Retrieved fields are saved as Field_*.mat in the field_retrieval/ folder.
   • Six representative phase maps and a central cross-section from 150 angles are also saved as Field_*.png.
5. Click on the displayed phase delay map to begin marking sample regions. Click and drag around the sample area to draw a sample mask—masked regions appear in semi-transparent white. You can adjust the mask size using the mouse scroll wheel. Use the toggle to switch between "Draw" and "Erase" modes as needed. When finished, click "Stop Masking" to complete the process.

3. Tomogram Reconstruction (Blue Box)

1. After field retrieval, proceed to tomogram reconstruction.
2. Use "Field Inspection" to examine and optionally exclude corrupted frames (e.g., those affected by dust or artifacts).
   • Set thresholds for:
     • Phase value (red line)
     • Phase gradient (green line)
   • Frames exceeding these thresholds will be excluded for tomogram reconstruction.
3. Click "Reconstruct" to begin reconstruction. Progress is displayed live.
4. Tomogram reconstruction for a single sample typically takes 2–3 minutes, depending on your system’s specifications.
5. Once completed:
   • A cross-sectional slice (x-y, y-z, or x-z) of the latest sample is displayed.
   • Navigate through different planes using the GUI.
   • Tomograms are saved as Tomogram_*.mat in the field_retrieval/ folder.
   • Cross-sectional slices and maximum projection images are also saved.
6. Export to TIFF:
   • Click "Export TIFF" to generate 16-bit stackable TIFF files readable by ImageJ/FIJI.
   • Refractive index (RI) values are scaled by 10,000 (e.g., RI 1.344 → value 13440).
   • Axial and lateral resolutions differ and can be checked from the variables res3 (lateral) and res4 (axial) in the .mat file.
   • Because the voxel size is anisotropic, be sure to adjust scaling properly in ImageJ/FIJI.

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Citation

If you use ODT_FieldTomogramGUI in your research or publication, please cite it as:

Kyoohyun Kim (2025). ODT_FieldTomogramGUI version X.X.X: MATLAB GUI for Field Retrieval and Tomogram Reconstruction in Optical Diffraction Tomography [Software]. Available at: https://github.com/OpticalDiffractionTomography/ODT_FieldTomogramGUI