https://github.com/sydney-informatics-hub/tiff2vrml

Takes a stack of TIFF files and converts to a 3D VRML file
https://github.com/sydney-informatics-hub/tiff2vrml

Last synced: over 1 year ago
JSON representation

Takes a stack of TIFF files and converts to a 3D VRML file

• Host: GitHub
• URL: https://github.com/sydney-informatics-hub/tiff2vrml
• Owner: Sydney-Informatics-Hub
• Created: 2023-11-05T21:59:35.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2023-11-16T11:50:54.000Z (over 2 years ago)
• Last Synced: 2025-01-22T11:13:05.422Z (over 1 year ago)
• Language: Jupyter Notebook
• Size: 383 KB
• Stars: 1
• Watchers: 6
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

          

# Helper code

```

import numpy as np

import tifffile as tiff

import os

import scipy

import matplotlib.pyplot as plt

# Read the tiff files, assume have sorteable filenames 001.tif, 002.tif etc.

tiff_dir = "data/"

tiff_files = [f for f in os.listdir(tiff_dir) if f.endswith(".tif")]

tiff_files.sort()

# Load the first TIFF file to get its dimensions

first_tiff = tiff_files[0]

height, width = first_tiff.shape

num_slices = len(tiff_files)

# Create a numpy array to store the volume

volume = np.zeros((height, width, num_slices), dtype=np.uint8)

# Iterate through TIFF files and populate a volume

for i, tiff_file in enumerate(tiff_files):

  print(tiff_file)

  tiff_data = tiff.imread(os.path.join(tiff_dir, tiff_file))

  volume[:, :, i] = tiff_data

```

# Try

* Open3d

* vtk

* ?? others

# Now do magic

Export vrml