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from pystackreg import StackReg
import numpy as np
import imageio.v2 as iio
from PIL import Image
def get_sr_mode(mode_str): return {
"TRANSLATION": StackReg.TRANSLATION,
"RIGID_BODY": StackReg.RIGID_BODY,
"SCALED_ROTATION": StackReg.SCALED_ROTATION,
"AFFINE": StackReg.AFFINE,
"BILINEAR": StackReg.BILINEAR,
}.get(mode_str, StackReg.RIGID_BODY)
def normalize_stack(stack):
norm_stack = []
for frame in stack:
f = frame.astype(np.float32)
low, high = np.percentile(f, (1, 99))
f = np.clip(f, low, high)
f = (f - f.min()) / (np.ptp(f) + 1e-8) * 255 if np.ptp(f) > 0 else np.zeros_like(f)
norm_stack.append(f.astype(np.uint8))
return np.stack(norm_stack)
def upscale(image, factor=3):
return image.resize((image.width * factor, image.height * factor), Image.NEAREST)
def load_stack(file):
stack = np.array(iio.mimread(file))
if stack.ndim == 4 and stack.shape[-1] == 3:
stack = np.mean(stack, axis=-1)
return normalize_stack(stack)
##### Markdowns #####
citation_markdown = """
### 📘 Credits & Acknowledgments
Register TIFF stacks using multiple alignment strategies.
**App Author**: [Quentin Chappuis](https://github.com/qchapp)
**Pystackreg Author**: [Gregor Lichtenberg](https://github.com/glichtner)
🔗 [Pystackreg on GitHub](https://github.com/glichtner/pystackreg)
**Original Algorithm Author**: Philippe Thévenaz (EPFL)
The core algorithm was originally developed by Philippe Thévenaz and is described in the following publication:
> P. Thévenaz, U.E. Ruttimann, M. Unser
> *A Pyramid Approach to Subpixel Registration Based on Intensity*
> *IEEE Transactions on Image Processing*, vol. 7, no. 1, pp. 27–41, January 1998.
> 🔗 [View paper](http://bigwww.epfl.ch/publications/thevenaz9801.html)
"""
documentation_markdown = """
### Overview
This app provides three registration modes for 2D TIFF image stacks using the `pystackreg` library.
---
### 📚 Tab 1: Reference-Based Alignment
Register a stack using a reference frame. You can:
- Use a frame from the **same stack** as reference
- Or upload an **external reference stack**
1. Upload the stack you want to align.
2. (Optional) Check "Use external reference stack" to align to a frame from another file.
3. Choose the reference frame using the slider.
4. (Optional) Choose transformation mode.
5. Click **▶️ Align Stack**.
6. Use sliders to browse original/aligned results and download the output.
---
### 🎯 Tab 2: Stack-Based Alignment
Align one stack (moving) to another (reference).
1. Upload both **reference** and **moving** stacks.
2. (Optional) Choose transformation mode.
3. Click **▶️ Register** to align.
4. Browse and download registered stack.
---
### 🧩 Tab 3: Frame-to-Frame Alignment
Align a **single frame to another** from the same stack.
1. Upload a stack.
2. Select **reference** and **moving** frames using sliders.
3. Choose transformation mode.
4. Click **▶️ Register Frame**.
5. View/download the result.
---
### 🔄 Reset Buttons
Each tab includes a **Reset Tab** button that clears inputs, outputs, and internal state.
---
### 🧠 Credits
App developed by **Quentin Chapuis**
Library: [`pystackreg`](https://github.com/glichtner/pystackreg) by **Georg Lichtenberg**
""" |