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replace and autoformat #90

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2 changes: 1 addition & 1 deletion .gitmodules
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
[submodule "bioio_czi/czi-to-ome-xslt"]
path = bioio_czi/czi-to-ome-xslt
url = https://github.com/AllenCellModeling/czi-to-ome-xslt.git
url = https://github.com/bioio-devs/czi-to-ome-xslt.git
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@kmitcham kmitcham Mar 17, 2026

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This is intentional, and not auto formatting, right?

41 changes: 25 additions & 16 deletions README.md
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Expand Up @@ -9,7 +9,6 @@ A BioIO reader plugin for reading CZIs using `pylibczirw` (default) or `aicspyli

---


## Documentation

[See the bioio documentation on our GitHub pages site](https://bioio-devs.github.io/bioio/OVERVIEW.html) - the general use and installation instructions there will work for this package.
Expand All @@ -29,29 +28,32 @@ Install bioio-czi alongside bioio:
**Development Head:** `pip install git+https://github.com/bioio-devs/bioio-czi.git`

## pylibczirw vs. aicspylibczi
`bioio-czi` can operate in [pylibczirw](https://github.com/ZEISS/pylibczirw) mode (the default) or [aicspylibczi](https://github.com/AllenCellModeling/aicspylibczi) mode.

| Feature | pylibczirw mode | aicspylibczi mode |
|--|--|--|
| Read CZIs from the internet | ✅ | ❌ |
| Read single tile from tiled CZI | ❌ | ✅ |
| Read single tile's metadata from tiled CZI | ❌ | ✅ |
| Read elapsed time metadata* | ❌ | ✅ |
| Handle CZIs with different dimensions per scene** | ❌ | ✅ |
| Read stitched mosaic of a tiled CZI | ✅ | ✅ |
`bioio-czi` can operate in [pylibczirw](https://github.com/ZEISS/pylibczirw) mode (the default) or [aicspylibczi](https://github.com/bioio-devs/aicspylibczi) mode.
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@toloudis toloudis Mar 16, 2026

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all changes except for this line are just auto-formatting.


| Feature | pylibczirw mode | aicspylibczi mode |
| --------------------------------------------------- | --------------- | ----------------- |
| Read CZIs from the internet | ✅ | ❌ |
| Read single tile from tiled CZI | ❌ | ✅ |
| Read single tile's metadata from tiled CZI | ❌ | ✅ |
| Read elapsed time metadata\* | ❌ | ✅ |
| Handle CZIs with different dimensions per scene\*\* | ❌ | ✅ |
| Read stitched mosaic of a tiled CZI | ✅ | ✅ |

The primary difference is that `pylibczirw` supports reading CZIs over the internet but cannot access individual tiles from a tiled CZI. To use `aicspylibczi`, add the `use_aicspylibczi=True` parameter when creating a reader. For example: `from bioio import BioImage; img = BioImage(..., use_aicspylibczi=True)`.

*Elapsed time metadata include the following. These are derived from individual subblock metadata.
* `BioImage(...).time_interval`
* `BioImage(...).standard_metadata.timelapse_interval`
* `BioImage(...).standard_metadata.total_time_duration`
\*Elapsed time metadata include the following. These are derived from individual subblock metadata.

**The underlying pylibczirw reader only exposes per-scene X and Y dimensions. Files that do not have consistent dimensions per scene may be read incorrectly in pylibczirw mode.
- `BioImage(...).time_interval`
- `BioImage(...).standard_metadata.timelapse_interval`
- `BioImage(...).standard_metadata.total_time_duration`

\*\*The underlying pylibczirw reader only exposes per-scene X and Y dimensions. Files that do not have consistent dimensions per scene may be read incorrectly in pylibczirw mode.

## Example Usage (see full documentation for more examples)

### Basic usage

```python
from bioio import BioImage

Expand All @@ -63,9 +65,11 @@ path = (
img = BioImage(path)
print(img.shape) # (1, 1, 1, 5684, 5925)
```

Note: accessing files from the internet is not available in `aicspylibczi` mode.

### Individual tiles with aicspylibczi

```python
img = BioImage(
"S=2_4x2_T=2=Z=3_CH=2.czi",
Expand All @@ -78,21 +82,26 @@ subblocks = img.metadata.findall("./Subblocks/Subblock")
print(len(subblocks)) # 192
print(img.get_image_data("TCZYX", M=3).shape) # (2, 2, 3, 256, 256)
```

The `M` dimension is used to select a specific tile.

### Stitched mosaic with pylibczirw

```python
img = BioImage("S=2_4x2_T=2=Z=3_CH=2.czi")
print(img.dims) # <Dimensions [T: 2, C: 2, Z: 3, Y: 487, X: 947]>
```

All 8 tiles are stitched together. Where tiles overlap, the pixel value is the pixel value from the tile with the highest M-index.

### Explicit Reader

This example shows a simple use case for just accessing the pixel data of the image
by explicitly passing this `Reader` into the `BioImage`. Passing the `Reader` into
the `BioImage` instance is optional as `bioio` will automatically detect installed
plug-ins and auto-select the most recently installed plug-in that supports the file
passed in.

```python
from bioio import BioImage
import bioio_czi
Expand All @@ -102,8 +111,8 @@ img.data
```

## Issues
[_Click here to view all open issues in bioio-devs organization at once_](https://github.com/search?q=user%3Abioio-devs+is%3Aissue+is%3Aopen&type=issues&ref=advsearch) or check this repository's issue tab.

[_Click here to view all open issues in bioio-devs organization at once_](https://github.com/search?q=user%3Abioio-devs+is%3Aissue+is%3Aopen&type=issues&ref=advsearch) or check this repository's issue tab.

## Development

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