https://github.com/kaczmarj/tyler
Extract tiles from whole slide images.
https://github.com/kaczmarj/tyler
Last synced: 2 months ago
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Extract tiles from whole slide images.
- Host: GitHub
- URL: https://github.com/kaczmarj/tyler
- Owner: kaczmarj
- License: apache-2.0
- Created: 2021-04-28T03:00:06.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2021-09-30T19:31:03.000Z (over 3 years ago)
- Last Synced: 2025-02-10T02:33:32.000Z (4 months ago)
- Language: Python
- Size: 23.4 KB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# tyler
Python module to extract tiles from whole slide images.
# Examples
## Command-line
```bash
python -m tyler \
-o test-tiles \
--tile-size 1000 1000 \
wsi.svs mask.png
```
## In a Python script
```python
import openslide
import PIL
import tyler
slide = openslide.OpenSlide(
"TCGA-02-0010-01Z-00-DX4.07de2e55-a8fe-40ee-9e98-bcb78050b9f7.svs"
)
print("Slide dimensions (cols, rows): ", slide.dimensions)
tiles = tyler.get_tiles(
oslide=slide,
wsi_id="TCGA-02-0010-01Z-00-DX4.07de2e55-a8fe-40ee-9e98-bcb78050b9f7",
level=0,
tile_size=(1000, 1000),
)
print("Number of tiles (cols, rows):", tiles.shape)
# Plot the top-left tile.
tiles[0, 0].to_pil_image()
# Save to disk.
tiles[0, 0].to_png("top-left-tile.png")
# Read the PNG and get its metadata.
# Tyler is generous and saves important metadata within the PNG file.
img = PIL.Image.open("top-left-tile.png")
print("Image metadata")
for key, value in img.text.items():
print(f" {key}: {value}")
```
The output of the preceding code
```
Slide dimensions (cols, rows): (32001, 38474)
Number of tiles (cols, rows): (32, 38)
Image metadata
oslide: OpenSlide('TCGA-02-0010-01Z-00-DX4.07de2e55-a8fe-40ee-9e98-bcb78050b9f7.svs')
wsi_id: TCGA-02-0010-01Z-00-DX4.07de2e55-a8fe-40ee-9e98-bcb78050b9f7
c: 0
r: 0
cols: 1000
rows: 1000
level: 0
timestamp: 1619631433
```
# Installation
Install with `pip`:
```bash
python -m pip install --no-cache-dir https://github.com/kaczmarj/tyler/tarball/main
```
Tyler depends on [OpenSlide](https://openslide.org/), which must be installed separately. See [OpenSlide's download page](https://openslide.org/download/) for more information.
## Developer installation
Create a virtual environment, and install development dependencies.
```bash
git clone https://github.com/kaczmarj/tyler
cd tyler
python -m venv venv
source ./venv/bin/activate
python -m pip install --no-cache-dir --editable .[dev]
```
# Musings on data orientation
- Openslide `slide.dimensions` orients data as `(cols, rows)`.
- PIL orients data as `(cols, rows)`.
- Scikit-image orients data as `(rows, cols, channels)`.
- Matplotlib pyplot imshow expects data as `(rows, cols, [channels])`.
where `[]` indicates optional axis.
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