You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Copy file name to clipboardExpand all lines: README.md
+13-11Lines changed: 13 additions & 11 deletions
Display the source diff
Display the rich diff
Original file line number
Diff line number
Diff line change
@@ -155,8 +155,7 @@ Axis squeezing and cache generation are performed explicitly and transparently.
155
155
OMIO provides utility functions to create empty metadata and image templates that can be populated programmatically or used as blueprints for new datasets.
156
156
157
157
## Expected project structure (BIDS-like)
158
-
OMIO supports batch processing of projects organized in a BIDS-like manner.
159
-
An abstract example is shown below:
158
+
OMIO supports batch processing of projects organized in a BIDS-like manner. An abstract example is shown below:
explicit subject IDs or subject-prefix discovery, arbitrary folder-token levels,
228
-
file-pattern filtering, name-based exclusion, skip-if-already-converted behavior, and
229
-
persistent run/error reports in the project root.
230
-
Use `output_folder_name` for relative or absolute output locations; `save_options`
231
-
is reserved for writer settings such as `overwrite` or `compression_level`.
232
-
OME-TIFF multi-file series are collapsed during discovery by default, and optional
233
-
`folder_stacks` tags can be used to merge tagged stack folders before processing.
224
+
`bids_batch_process()` supports explicit subject IDs or subject-prefix discovery, arbitrary folder-token levels, file-pattern filtering, name-based exclusion, skip-if-already-converted behavior, and persistent run/error reports in the project root. Use `output_folder_name` for relative or absolute output locations; `save_options` is reserved for writer settings such as `overwrite` or `compression_level`. OME-TIFF multi-file series are collapsed during discovery by default, and optional `folder_stacks` tags can be used to merge tagged stack folders before processing.
234
225
235
226
```python
236
227
result = omio.bids_batch_process(
@@ -278,6 +269,17 @@ OMIO relies on the following third-party libraries for file format handling:
A comprehensive documentation website is available at: <https://omio.readthedocs.io>
274
+
275
+
The repository folder `additional_scripts` contains example scripts and Jupyter notebooks that demonstrate typical usage patterns, including:
276
+
277
+
*`usage_example_interactive.py`
278
+
*`usage_example_interactive.ipynb`
279
+
280
+
Both scripts demonstrate interactive usage of OMIO in a Python script, including reading, merging, writing, and visualization in napari. Also included: Zarr-backed caching, BIDS-like batch processing, and Thorlabs RAW YAML sidecar generation, empty metadata and image templates, and OME-compliance checks upon writing.
281
+
282
+
281
283
## Requests for new file formats and reader extensions
282
284
OMIO is designed to grow and evolve based on user needs and real-world microscopy data. By intention, we will add support for additional file formats or format variants over time, bases on user requests and contributions.
0 commit comments