Documentation for v0.2.0

README.md

 # QIM3D (Quantitative Imaging in 3D)
 
-QIM is a Python library for 3D quantitative imaging analysis. It provides functionality for handling data, as well as tools for visualization and analysis.
+`qim3D` is a Python library for quantitative imaging analysis in 3D. It provides functionality for handling data, as well as tools for visualization and analysis.
+
+This library contains the tools and functionalities of the QIM platform, accessible at https://qim.dk/platform
 
- 
 ## Installation
 
-Install using pip:
+Install the latest stable version by using pip:
 
 ```bash
 pip install qim3d
 ```
 
- 
+Or clone this repository for the most recent version.
+
+
 # Usage
+Some basic funtionalites are descibred here, for the full functionatilies please see the documentation.
 
- 
 ## Loading Data
 To load image data from a file, use `qim.io.load()`
 
 ```python
 import qim3d
 
-# Load a TIFF file
+# Load a file
 vol = qim3d.io.load("path/to/file.tif")
 
-# Load a TIFF file as a virtual stack
+# Load a file as a virtual stack
 vol = qim3d.io.load("path/to/file.tif", virtual_stack=True)
 ```
 
- 
+## Visualize data
+YOu can easily check slices from your volume using `slice_viz`
+
+```python
+import qim3d
+
+img = qim3d.examples.fly_150x256x256
+
+# By default shows the middle slice
+qim3d.viz.slice_viz(img)
+
+# Or we can specifly positions
+qim3d.viz.slice_viz(img, position=[0,32,128])
+
+# Parameters for size and colormap are also possible
+qim3d.viz.slice_viz(img, img_width=6, img_height=6, cmap="inferno")
+
+```
+
+
 ## GUI Components
-QIM provides GUI components for interactive data exploration. The `qim3d.gui` module contains various classes for visualization and analysis:
+The library also provides GUI components for interactive data exploration. 
+The `qim3d.gui` module contains various classes for visualization and analysis:
 
 ```python
 import qim3d
@@ -39,16 +62,8 @@ app = qim3d.gui.iso3d.Interface()
 app.launch()
 ```
 
-Graphical interfaces currently available:
-- Data exploration tool (`qim3d.gui.data_exploration`)
-- 3D visualization with isosurfaces (`qim3d.gui.iso3d`)
-- Local thickness (`qim3d.gui.local_thickness`)
-
-
- 
 # Contributing
 Contributions to QIM are welcome! If you find a bug, have a feature request, or would like to contribute code, please open an issue or submit a pull request.
 
- 
 # License
 This project is licensed under the MIT License.
\ No newline at end of file

docs/version_history.md

+# Release history
+Here you can fin details about the version history of `qim3d`
+
+
+## v0.2.0 (Sept 18, 2023)
+```pip install qim3d==0.2.0```
+
+Includes new develoments toward the usability of the library, as well as its integration with the QIM platform.
+
+- Refactored code for the graphical interfaces
+    - For the local thicknes GUI, now it is possible to pass and receive numpy arrays instead of using the upload functionality.
+- Improved data loader
+    - Now the extensions `tif`, `h5` and `txm` are supported.
+- Added `qim3d.viz.slice_viz` for easy slice visualization.
+- U-net model creation
+    - Model availabe from `qim3d.models.UNet`
+    - Data augmentation class at `qim3d.utils.Augmentation`
+    - Notebook with full pipeline at `docs/notebooks/Unet.ipynb`
+- Image examples accessible from `qim3d.examples`
+
+
+## v0.1.3 (May 17, 2023)
+```pip install qim3d==0.1.3```
+
+First stable release.
+
+- Simple Tiff data loader
+- Graphical interfaces
+    - Local thickness
+    - 3D Isosurfaces
+    - Data exploration tool
\ No newline at end of file