Added option to crop image stacks and process only central frames

Author: tieneupin

src/murfey/server/api/clem.py

@@ -702,6 +702,7 @@ class AlignAndMergeParams(BaseModel):
     images: list[Path]
     metadata: Path
     # Optional processing parameters
+    crop_to_n_frames: Optional[int] = None
     align_self: Optional[str] = None
     flatten: Optional[Literal["min", "max", "mean"]] = "mean"
     align_across: Optional[str] = None
@@ -754,6 +755,7 @@ def align_and_merge_stacks(
         images=align_and_merge_params.images,
         metadata=align_and_merge_params.metadata,
         # Optional processing parameters
+        crop_to_n_frames=align_and_merge_params.crop_to_n_frames,
         align_self=align_and_merge_params.align_self,
         flatten=align_and_merge_params.flatten,
         align_across=align_and_merge_params.align_across,

src/murfey/workflows/clem/align_and_merge.py

@@ -25,6 +25,7 @@ def submit_cluster_request(
     images: list[Path],
     metadata: Path,
     # Optional processing parameters
+    crop_to_n_frames: Optional[int] = None,
     align_self: Optional[str] = None,
     flatten: Optional[Literal["min", "max", "mean"]] = "mean",
     align_across: Optional[str] = None,
@@ -64,6 +65,7 @@ def submit_cluster_request(
                 "series_name": series_name,
                 "images": [str(file) for file in images],
                 "metadata": str(metadata),
+                "crop_to_n_frames": crop_to_n_frames,
                 "align_self": align_self,
                 "flatten": flatten,
                 "align_across": align_across,

src/murfey/workflows/clem/register_preprocessing_results.py

@@ -187,6 +187,7 @@ def register_lif_preprocessing_result(
             series_name=result.series_name,
             images=image_stacks,
             metadata=result.metadata,
+            crop_to_n_frames=50,
             align_self="enabled",
             flatten="mean",
             align_across="enabled",
@@ -369,6 +370,7 @@ def register_tiff_preprocessing_result(
             series_name=result.series_name,
             images=image_stacks,
             metadata=result.metadata,
+            crop_to_n_frames=50,
             align_self="enabled",
             flatten="mean",
             align_across="enabled",