lbm_suite2p_python 2.5.3__tar.gz → 2.5.7__tar.gz

{lbm_suite2p_python-2.5.3/lbm_suite2p_python.egg-info → lbm_suite2p_python-2.5.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lbm_suite2p_python
-Version: 2.5.3
+Version: 2.5.7
 Summary: Light Beads Microscopy Pipeline using Suite2p
 License-Expression: BSD-3-Clause
 Project-URL: homepage, https://github.com/MillerBrainObservatory/LBM-Suite2p-Python
@@ -8,12 +8,12 @@ Keywords: Pipeline,Numpy,Microscopy,ScanImage,Suite2p,tiff
 Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Science/Research
 Classifier: Programming Language :: Python :: 3 :: Only
-Requires-Python: <3.12.10,>=3.12.7
+Requires-Python: <3.14,>=3.12.7
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
-Requires-Dist: mbo_utilities>=2.5.1
-Provides-Extra: suite2p
-Requires-Dist: suite2p_mbo>=2.0.1; extra == "suite2p"
+Requires-Dist: mbo_utilities>=2.6.3
+Requires-Dist: suite2p_mbo>=2.0.1
+Requires-Dist: setuptools<81
 Provides-Extra: rastermap
 Requires-Dist: rastermap; extra == "rastermap"
 Provides-Extra: cellpose
@@ -22,7 +22,7 @@ Provides-Extra: torch
 Requires-Dist: torch>=2.7.0; extra == "torch"
 Requires-Dist: torchvision>=0.22.0; extra == "torch"
 Provides-Extra: all
-Requires-Dist: lbm_suite2p_python[cellpose,rastermap,suite2p,torch]; extra == "all"
+Requires-Dist: lbm_suite2p_python[cellpose,rastermap,torch]; extra == "all"
 Dynamic: license-file
 
 <p align="center">

{lbm_suite2p_python-2.5.3 → lbm_suite2p_python-2.5.7}/lbm_suite2p_python/__init__.py

@@ -9,11 +9,6 @@ from lbm_suite2p_python.run_lsp import (
     generate_plane_dirname,
 )
 
-# Cellpose workflow exports
-from lbm_suite2p_python.cellpose_workflow import (
-    redetect,
-    enhance_summary_image,
-)
 from lbm_suite2p_python.cellpose import (
     train_cellpose,
     annotate,
@@ -81,7 +76,6 @@ from lbm_suite2p_python import (
     conversion,
     utils,
     postprocessing,
-    normcorre,
 )
 
 try:
@@ -100,8 +94,6 @@ __all__ = [
     "generate_plane_dirname",
 
     # Cellpose / HITL Workflow
-    "redetect",
-    "enhance_summary_image",
     "train_cellpose",
     "annotate",
     "open_in_gui",
@@ -119,7 +111,6 @@ __all__ = [
     "conversion",
     "utils",
     "postprocessing",
-    "normcorre",
 
     # Grid Search
     "grid_search",

{lbm_suite2p_python-2.5.3 → lbm_suite2p_python-2.5.7}/lbm_suite2p_python/cellpose.py

@@ -37,9 +37,10 @@ def _compute_projection(
     Parameters
     ----------
     arr : array-like
-        Input array (T, Y, X) for 3D or (T, Z, Y, X) for 4D.
+        Input array. mbo_utilities arrays are 5D TCZYX.
+        Legacy 4D TZYX and 3D TYX inputs are also supported.
     plane_idx : int, optional
-        For 4D arrays, which z-plane to extract (0-indexed).
+        For volumetric arrays, which z-plane to extract (0-indexed).
         If None, uses all planes for 3D segmentation.
     method : str
         Projection method: 'max', 'mean', 'std', or 'percentile'.
@@ -53,19 +54,23 @@ def _compute_projection(
     """
     ndim = len(arr.shape)
 
-    if ndim == 4:
-        # (T, Z, Y, X)
+    if ndim == 5:
+        # 5D TCZYX: use channel 0
+        if plane_idx is not None:
+            data = arr[:, 0, plane_idx, :, :]  # (T, Y, X)
+        else:
+            data = arr[:, 0, :, :, :]  # (T, Z, Y, X)
+    elif ndim == 4:
+        # legacy 4D TZYX
         if plane_idx is not None:
-            # extract single plane -> (T, Y, X)
             data = arr[:, plane_idx, :, :]
         else:
-            # keep all planes -> (T, Z, Y, X)
             data = arr[:]
     elif ndim == 3:
-        # (T, Y, X)
+        # legacy 3D TYX
         data = arr[:]
     else:
-        raise ValueError(f"Expected 3D or 4D array, got {ndim}D")
+        raise ValueError(f"Expected 3D, 4D, or 5D array, got {ndim}D")
 
     # convert to numpy if lazy
     if hasattr(data, "compute"):
@@ -577,18 +582,18 @@ def cellpose(
 
     # get array info
     shape = arr.shape
-    ndim = len(shape)
     num_planes = _get_num_planes(arr)
     num_frames = shape[0]
+    is_volumetric = num_planes > 1
 
     print(f"\nDataset info:")
     print(f"  Shape: {shape}")
     print(f"  Frames: {num_frames}")
     print(f"  Planes: {num_planes}")
-    print(f"  Data type: {'4D volumetric' if ndim == 4 else '3D planar'}")
+    print(f"  Data type: {'volumetric' if is_volumetric else 'planar'}")
 
     # normalize planes to 0-indexed list
-    if ndim == 4:
+    if is_volumetric:
         planes_to_process = _normalize_planes(planes, num_planes)
     else:
         planes_to_process = [None]  # single plane data