lbm_suite2p_python 2.0.0__tar.gz → 2.0.1__tar.gz

{lbm_suite2p_python-2.0.0/lbm_suite2p_python.egg-info → lbm_suite2p_python-2.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lbm_suite2p_python
-Version: 2.0.0
+Version: 2.0.1
 Summary: Light Beads Microscopy Pipeline using Suite2p
 License-Expression: BSD-3-Clause
 Project-URL: homepage, https://github.com/MillerBrainObservatory/LBM-Suite2p-Python
@@ -11,15 +11,7 @@ Classifier: Programming Language :: Python :: 3 :: Only
 Requires-Python: <3.12.10,>=3.12.7
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
-Requires-Dist: mkl_fft
-Requires-Dist: mbo_utilities[gui,suite3d]>=1.0.7
-Requires-Dist: suite2p_mbo
-Requires-Dist: tqdm
-Requires-Dist: pandas
-Requires-Dist: matplotlib
-Requires-Dist: dask>=2025.9.1
-Requires-Dist: zarr==3.1.3
-Requires-Dist: seaborn>=0.13.2
+Requires-Dist: mbo_utilities>=2.0.2
 Provides-Extra: cpsam
 Requires-Dist: cellpose==4.0.6; extra == "cpsam"
 Requires-Dist: pytorch; extra == "cpsam"
@@ -38,11 +30,11 @@ Dynamic: license-file
 
 [![Documentation](https://img.shields.io/badge/Documentation-blue?style=for-the-badge&logo=readthedocs&logoColor=white)](https://millerbrainobservatory.github.io/LBM-Suite2p-Python/index.html)
 
-This package is still in a *beta* stage of development.
+This package is still in a *late-beta* stage of development.
 
-A pipeline for processing 2-photon Light Beads Microscopy (LBM) datasets.
+A pipeline for processing volumetric 2-photon Light Beads Microscopy (LBM) datasets.
 
-This pipeline uses the following software:
+This pipeline uses the following open-source software:
 
 - [suite2p](https://github.com/MouseLand/suite2p)
 - [cellpose](https://github.com/MouseLand/cellpose)
@@ -57,30 +49,33 @@ This pipeline uses the following software:
 
 ## Installation
 
-See the [installation documentation](https://millerbrainobservatory.github.io/LBM-Suite2p-Python/install.html) for more details.
+This pipeline is installable with `pip`:
 
-This pipeline is fully installable with `pip`.
+```bash
+pip install lbm_suite2p_python
+# with uv: uv pip install lbm_suite2p_python
+```
 
-`conda` can still be used for the virual environment, but be mindful to only install packages with `conda install` when absolutely necessary.
+We highly encourage the use of a virtual environment. If you are unfamiliar with virtual environments, see our documentation [here](https://millerbrainobservatory.github.io/mbo_utilities/venvs.html).
 
-We recommend cloning the repository, until a more established workflow is available to upload to PyPi.
+You may also use git to clone and install locally for updates not yet released to pypi:
 
-```
+```bash
 git clone https://github.com/MillerBrainObservatory/LBM-Suite2p-Python.git
-git clone https://github.com/Suite3D # TODO
 cd LBM-Suite2p-Python
 
 # make sure your virtual environment is active
-pip install ".[all]"  # optional, contains ".[gui, notebook]"
+pip install "." 
 ```
 
 ## Issues
+
 Widgets may throw "Invalid Rect" errors. This can be safely ignored until it is [resolved](https://github.com/pygfx/wgpu-py/issues/716#issuecomment-2880853089).
 
 ---
 
 ## Acknowledgements
 
-Thank you to the developers of [scanreader](https://github.com/atlab/scanreader), which provides a clean interface to ScanImage metadata using only tifffile and numpy.
+This pipeline is mostly a volumetric wrapper around [suite2p](https://github.com/MouseLand/suite2p), [cellpose](https://github.com/MouseLand/cellpose) and [Suite3D](https://github.com/alihaydaroglu/suite3d). We thank the contributors to those projects.
 
-We vendor this repository because it is not published to an indexable Python package registry like PyPI.
+Thank you to the developers of [scanreader](https://github.com/atlab/scanreader), which provides a clean interface to ScanImage metadata using only tifffile and numpy.

{lbm_suite2p_python-2.0.0 → lbm_suite2p_python-2.0.1}/README.md

@@ -4,11 +4,11 @@
 
 [![Documentation](https://img.shields.io/badge/Documentation-blue?style=for-the-badge&logo=readthedocs&logoColor=white)](https://millerbrainobservatory.github.io/LBM-Suite2p-Python/index.html)
 
-This package is still in a *beta* stage of development.
+This package is still in a *late-beta* stage of development.
 
-A pipeline for processing 2-photon Light Beads Microscopy (LBM) datasets.
+A pipeline for processing volumetric 2-photon Light Beads Microscopy (LBM) datasets.
 
-This pipeline uses the following software:
+This pipeline uses the following open-source software:
 
 - [suite2p](https://github.com/MouseLand/suite2p)
 - [cellpose](https://github.com/MouseLand/cellpose)
@@ -23,30 +23,33 @@ This pipeline uses the following software:
 
 ## Installation
 
-See the [installation documentation](https://millerbrainobservatory.github.io/LBM-Suite2p-Python/install.html) for more details.
+This pipeline is installable with `pip`:
 
-This pipeline is fully installable with `pip`.
+```bash
+pip install lbm_suite2p_python
+# with uv: uv pip install lbm_suite2p_python
+```
 
-`conda` can still be used for the virual environment, but be mindful to only install packages with `conda install` when absolutely necessary.
+We highly encourage the use of a virtual environment. If you are unfamiliar with virtual environments, see our documentation [here](https://millerbrainobservatory.github.io/mbo_utilities/venvs.html).
 
-We recommend cloning the repository, until a more established workflow is available to upload to PyPi.
+You may also use git to clone and install locally for updates not yet released to pypi:
 
-```
+```bash
 git clone https://github.com/MillerBrainObservatory/LBM-Suite2p-Python.git
-git clone https://github.com/Suite3D # TODO
 cd LBM-Suite2p-Python
 
 # make sure your virtual environment is active
-pip install ".[all]"  # optional, contains ".[gui, notebook]"
+pip install "." 
 ```
 
 ## Issues
+
 Widgets may throw "Invalid Rect" errors. This can be safely ignored until it is [resolved](https://github.com/pygfx/wgpu-py/issues/716#issuecomment-2880853089).
 
 ---
 
 ## Acknowledgements
 
-Thank you to the developers of [scanreader](https://github.com/atlab/scanreader), which provides a clean interface to ScanImage metadata using only tifffile and numpy.
+This pipeline is mostly a volumetric wrapper around [suite2p](https://github.com/MouseLand/suite2p), [cellpose](https://github.com/MouseLand/cellpose) and [Suite3D](https://github.com/alihaydaroglu/suite3d). We thank the contributors to those projects.
 
-We vendor this repository because it is not published to an indexable Python package registry like PyPI.
+Thank you to the developers of [scanreader](https://github.com/atlab/scanreader), which provides a clean interface to ScanImage metadata using only tifffile and numpy.

lbm_suite2p_python-2.0.1/lbm_suite2p_python/__init__.py

@@ -0,0 +1,30 @@
+from importlib.metadata import version, PackageNotFoundError
+
+from lbm_suite2p_python.default_ops import default_ops
+from lbm_suite2p_python.run_lsp import *
+from lbm_suite2p_python.utils import *
+from lbm_suite2p_python.volume import *
+from lbm_suite2p_python.zplane import *
+
+try:
+    __version__ = version("lbm_suite2p_python")
+except PackageNotFoundError:
+    # fallback for editable installs
+    __version__ = "0.0.0"
+
+__all__ = [
+    "run_volume",
+    "run_plane",
+    "plot_traces",
+    "plot_masks",
+    "plot_rastermap",
+    "plot_traces_noise",
+    "plot_volume_signal",
+    "plot_projection",
+    "plot_execution_time",
+    "plot_noise_distribution",
+    "dff_rolling_percentile",
+    "load_ops",
+    "load_planar_results",
+    "default_ops",
+]

lbm_suite2p_python-2.0.1/lbm_suite2p_python/merging.py

@@ -0,0 +1,282 @@
+from collections import defaultdict
+from pathlib import Path
+
+import numpy as np
+from tqdm.auto import tqdm
+
+from lbm_suite2p_python import plot_zplane_figures
+from mbo_utilities.lazy_array import Suite2pArray
+
+
+def group_plane_rois(input_dir):
+    input_dir = Path(input_dir)
+    grouped = defaultdict(list)
+
+    for d in input_dir.iterdir():
+        if (
+                d.is_dir()
+                and not d.name.endswith(".zarr")     # exclude zarr dirs
+                and d.stem.startswith("plane")
+                and "_roi" in d.stem
+        ):
+            parts = d.stem.split("_")
+            if len(parts) == 2 and parts[1].startswith("roi"):
+                plane = parts[0]  # e.g. "plane01"
+                grouped[plane].append(d)
+
+    return grouped
+
+
+def _merge_images(
+        ops_list,
+        keys_full=("refImg", "meanImg", "meanImgE"),
+        keys_cropped=("max_proj", "Vcorr"),
+):
+    merged = {}
+
+    # --- determine global dimensions
+    Ly = max(ops["Ly"] for ops in ops_list)
+    widths = [ops["Lx"] for ops in ops_list]
+    total_Lx = sum(widths)
+
+    # Full-FOV keys: tile horizontally
+    for key in keys_full:
+        if all(key in ops for ops in ops_list):
+            canvas = np.zeros((Ly, total_Lx), dtype=ops_list[0][key].dtype)
+            xoff = 0
+            for opsd in ops_list:
+                arr = opsd[key]
+                arr_h, arr_w = arr.shape
+                slot_w = opsd["Lx"]
+
+                # crop/pad vertically to Ly
+                crop_h = min(arr_h, Ly)
+                slot_h = Ly
+                tmp = np.zeros((slot_h, slot_w), dtype=arr.dtype)
+                tmp[:crop_h, :min(arr_w, slot_w)] = arr[:crop_h, :min(arr_w, slot_w)]
+
+                # insert into canvas
+                canvas[:slot_h, xoff:xoff + slot_w] = tmp
+                xoff += slot_w
+
+            merged[key] = canvas
+
+    # Cropped keys: place at yrange/xrange
+    for key in keys_cropped:
+        if all(key in ops for ops in ops_list):
+            canvas = np.zeros((Ly, total_Lx), dtype=ops_list[0][key].dtype)
+            xoff = 0
+            for opsd in ops_list:
+                arr = opsd[key]
+                arr_h, arr_w = arr.shape
+                yr = np.array(opsd.get("yrange", [0, Ly]))
+                xr = np.array(opsd.get("xrange", [0, opsd["Lx"]])) + xoff
+
+                slot_h = yr[1] - yr[0]
+                slot_w = xr[1] - xr[0]
+
+                tmp = np.zeros((slot_h, slot_w), dtype=arr.dtype)
+                tmp[:min(arr_h, slot_h), :min(arr_w, slot_w)] = arr[:min(arr_h, slot_h), :min(arr_w, slot_w)]
+
+                canvas[yr[0]:yr[0]+slot_h, xr[0]:xr[0]+slot_w] = tmp
+                xoff += opsd["Lx"]
+
+            merged[key] = canvas
+
+    return merged
+
+def merge_mrois(input_dir, output_dir, overwrite=True):
+    """
+    Merge Suite2p outputs from multiple ROIs into per-plane outputs.
+    Will attempt to merge everything available; skips missing files gracefully.
+    """
+    input_dir = Path(input_dir)
+    output_dir = Path(output_dir)
+    output_dir.mkdir(exist_ok=True)
+
+    grouped = group_plane_rois(input_dir)
+
+    for plane, dirs in tqdm(sorted(grouped.items()), desc="Merging mROIs", unit="plane"):
+        out_dir = output_dir / plane
+        out_ops = out_dir / "ops.npy"
+
+        if out_ops.exists() and not overwrite:
+            print(f"Skipping {plane}, merged outputs already exist")
+            continue
+
+        out_dir.mkdir(exist_ok=True)
+
+        # --- load per-ROI results
+        ops_list, stat_list, iscell_list = [], [], []
+        F_list, Fneu_list, spks_list = [], [], []
+        bin_paths = []
+        for d in sorted(dirs):
+            ops_path = d / "ops.npy"
+            if not ops_path.exists():
+                print(f"Skipping {d}, no ops.npy")
+                continue
+            ops = np.load(ops_path, allow_pickle=True).item()
+            ops_list.append(ops)
+
+            if (d / "stat.npy").exists():
+                stat_list.append(np.load(d / "stat.npy", allow_pickle=True))
+            if (d / "iscell.npy").exists():
+                iscell_list.append(np.load(d / "iscell.npy", allow_pickle=True))
+            if (d / "F.npy").exists():
+                F_list.append(np.load(d / "F.npy"))
+            if (d / "Fneu.npy").exists():
+                Fneu_list.append(np.load(d / "Fneu.npy"))
+            if (d / "spks.npy").exists():
+                spks_list.append(np.load(d / "spks.npy"))
+
+            if (d / "data_raw.bin").exists():
+                bin_paths.append(d / "data_raw.bin")
+            elif (d / "data.bin").exists():
+                bin_paths.append(d / "data.bin")
+
+        if not ops_list:
+            print(f"No valid ROIs found for {plane}, skipping merge")
+            continue
+
+        # --- dimensions
+        Ly = ops_list[0]["Ly"]
+        widths = [ops.get("xrange", [0, ops["Lx"]])[1] -
+                  ops.get("xrange", [0, ops["Lx"]])[0] for ops in ops_list]
+        total_Lx = int(sum(widths))
+
+        # --- merge stat + traces
+        stat = None
+        if stat_list:
+            for i, st in enumerate(stat_list):
+                xoff = int(sum(widths[:i]))
+                for s in st:
+                    s["xpix"] = np.asarray(s["xpix"], int) + xoff
+                    s["ypix"] = np.asarray(s["ypix"], int)
+                    s["med"] = [float(s["med"][0]), float(s["med"][1]) + xoff]
+                    if "lam" in s:
+                        s["lam"] = np.asarray(s["lam"], float).ravel()
+                    if "ipix_neuropil" in s:
+                        ypix, xpix = s["ypix"], s["xpix"]
+                        s["ipix_neuropil"] = ypix + xpix * Ly
+            stat = np.concatenate(stat_list)
+
+        iscell = np.concatenate(iscell_list, 0) if iscell_list else None
+        F = np.concatenate(F_list, 0) if F_list else None
+        Fneu = np.concatenate(Fneu_list, 0) if Fneu_list else None
+        spks = np.concatenate(spks_list, 0) if spks_list else None
+
+        # --- merge binary
+        merged_bin = out_dir / "data.bin"
+        if bin_paths:
+            arrays = [Suite2pArray(p) for p in bin_paths]
+            nframes = min(arr.nframes for arr in arrays)
+            dtype = arrays[0].dtype
+            with open(merged_bin, "wb") as f:
+                for i in range(nframes):
+                    frames = [arr[i] for arr in arrays]
+                    f.write(np.hstack(frames).astype(dtype).tobytes())
+            for arr in arrays:
+                arr.close()
+        else:
+            merged_bin = None
+
+        # --- merged ops header
+        merged_ops = dict(ops_list[0])
+        merged_ops.update({
+            "Ly": Ly,
+            "Lx": total_Lx,
+            "yrange": [0, Ly],
+            "xrange": [0, total_Lx],
+            "ops_path": str(out_ops.resolve()),
+            "save_path": str(out_dir.resolve()),
+            "nrois": len(ops_list),
+        })
+        if merged_bin:
+            merged_ops["reg_file"] = str(merged_bin.resolve())
+
+        # >>> THIS IS THE ONLY PLACE YOU MERGE IMAGES <<<
+        merged_ops.update(_merge_images(ops_list))
+
+        for key in ["yoff", "xoff", "corrXY", "badframes"]:
+            arrays = [ops[key] for ops in ops_list if key in ops]
+            if arrays and all(np.array_equal(a, arrays[0]) for a in arrays[1:]):
+                merged_ops[key] = arrays[0]
+
+        np.save(out_ops, merged_ops)
+        if stat is not None: np.save(out_dir / "stat.npy", stat)
+        if iscell is not None: np.save(out_dir / "iscell.npy", iscell)
+        if F is not None: np.save(out_dir / "F.npy", F)
+        if Fneu is not None: np.save(out_dir / "Fneu.npy", Fneu)
+        if spks is not None: np.save(out_dir / "spks.npy", spks)
+
+        try:
+            plot_zplane_figures(out_dir, run_rastermap=False)
+        except Exception:
+            pass
+
+
+def merge_zarr_rois(input_dir, output_dir=None, overwrite=True):
+    """
+    Concatenate roi1 + roi2 .zarr stores for each plane into a single planeXX.zarr.
+
+    Parameters
+    ----------
+    input_dir : Path or str
+        Directory containing planeXX_roi1, planeXX_roi2 subfolders with ops.npy + data.zarr.
+    output_dir : Path or str, optional
+        Where to write merged planeXX.zarr. Defaults to `input_dir`.
+    overwrite : bool
+        If True, existing outputs are replaced.
+    """
+    import dask.array as da
+
+    z_merged = None
+    input_dir = Path(input_dir)
+    output_dir = (
+        Path(output_dir)
+        if output_dir
+        else input_dir.parent / (input_dir.name + "_merged")
+    )
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+    roi1_dirs = sorted(input_dir.glob("*plane*_roi1*"))
+    roi2_dirs = sorted(input_dir.glob("*plane*_roi2*"))
+    if not roi1_dirs or not roi2_dirs:
+        print("No roi1 or roi2 in input dir")
+        return None
+    assert len(roi1_dirs) == len(roi2_dirs), "Mismatched ROI dirs"
+
+    for roi1, roi2 in zip(roi1_dirs, roi2_dirs):
+        zplane = roi1.stem.split("_")[0]  # "plane01"
+        out_path = output_dir / f"{zplane}.zarr"
+        if out_path.exists():
+            if overwrite:
+                import shutil
+
+                shutil.rmtree(out_path)
+            else:
+                print(f"Skipping {zplane}, {out_path} exists")
+                continue
+
+        # load ops
+        z1 = da.from_zarr(roi1)
+        z2 = da.from_zarr(roi2)
+
+        # sanity check
+        assert z1.shape[0] == z2.shape[0], "Frame count mismatch"
+        assert z1.shape[1] == z2.shape[1], "Height mismatch"
+
+        # concatenate along width (axis=2)
+        z_merged = da.concatenate([z1, z2], axis=2)
+        z_merged.to_zarr(out_path, overwrite=overwrite)
+
+    if z_merged:
+        print(f"{z_merged}")
+
+    return None
+
+
+if __name__ == "__main__":
+    fpath = Path(r"D:\W2_DATA\kbarber\07_27_2025\mk355\raw\anatomical_3_roi")
+    merge_mrois(fpath, fpath.parent / "anatomical_3_merged")
+    x = 2

{lbm_suite2p_python-2.0.0 → lbm_suite2p_python-2.0.1}/lbm_suite2p_python/postprocessing.py

@@ -6,7 +6,6 @@ from scipy.ndimage import percentile_filter
 from scipy.stats import norm
 
 
-import numpy as np
 
 def _normalize_iscell(iscell):
     """Ensure iscell is 1D boolean array."""
@@ -197,7 +196,7 @@ def ops_to_json(ops: dict | str | Path, outpath=None, indent=2):
     return outpath
 
 
-def normalize_traces(F, mode="per_neuron"):
+def normalize_traces(F, mode="percentile"):
     """
     Normalize fluorescence traces F to [0, 1] range.
     Parameters
@@ -429,3 +428,5 @@ def load_ops(ops_input: str | Path | list[str | Path]) -> dict:
         return ops_input
     print("Warning: No valid ops file provided, returning empty dict.")
     return {}
+
+

{lbm_suite2p_python-2.0.0 → lbm_suite2p_python-2.0.1}/lbm_suite2p_python/run_lsp.py

@@ -12,17 +12,17 @@ import numpy as np
 
 import suite2p
 from suite2p.io.binary import BinaryFile
-from lbm_suite2p_python.merging import remake_plane_figures
 from lbm_suite2p_python.postprocessing import (
     ops_to_json,
     load_planar_results,
     load_ops,
-    filter_by_area
 )
 from mbo_utilities.log import get as get_logger
-import mbo_utilities as mbo  # noqa
 
-from lbm_suite2p_python.zplane import save_pc_panels_and_metrics
+from lbm_suite2p_python.zplane import (
+    save_pc_panels_and_metrics,
+    plot_zplane_figures
+)
 
 logger = get_logger("run_lsp")
 
@@ -31,7 +31,6 @@ from lbm_suite2p_python.volume import (
     plot_volume_signal,
     plot_volume_neuron_counts,
     get_volume_stats,
-    plot_execution_time,
 )
 from mbo_utilities.file_io import get_plane_from_filename
 
@@ -90,7 +89,7 @@ def run_volume(
     ops: dict | str | Path = None,
     keep_reg: bool = True,
     keep_raw: bool = False,
-    force_reg: bool = True,
+    force_reg: bool = False,
     force_detect: bool = False,
     dff_window_size: int = 500,
     dff_percentile: int = 20,
@@ -162,6 +161,7 @@ def run_volume(
     - Traces animation over time and neurons
     - Optional rastermap clustering results
     """
+    from mbo_utilities.file_io import get_files, get_plane_from_filename
     start = time.time()
     if save_path is None:
         save_path = Path(input_files[0]).parent
@@ -173,8 +173,8 @@ def run_volume(
     for z, file in enumerate(input_files):
         tag = derive_tag_from_filename(Path(file).name)
         plane_num = get_plane_from_filename(tag, fallback=len(all_ops))
-        subdir = f"plane{plane_num:02d}"
-        plane_save_path = Path(save_path).joinpath(subdir)
+        # subdir = f"plane{tag:02d}"
+        plane_save_path = Path(save_path).joinpath(tag)
         plane_save_path.mkdir(exist_ok=True)
 
         start_file = time.time()
@@ -205,12 +205,16 @@ def run_volume(
 
     if "roi" in Path(input_files[0]).stem.lower():
         print("Detected mROI data, merging ROIs for each z-plane...")
-        from .merging import merge_mrois, remake_plane_figures
+        from .merging import merge_mrois
         merged_savepath = save_path.joinpath("merged_mrois")
         merge_mrois(save_path, merged_savepath)
-        all_ops = sorted(mbo.get_files(merged_savepath, "ops.npy", 2))
+        save_path = merged_savepath
 
-    print(f"Planes found after merge: {len(all_ops)}")
+        all_ops = sorted(get_files(merged_savepath, "ops.npy", 2))
+        print(f"Planes found after merge: {len(all_ops)}")
+    else:
+        all_ops = sorted(get_files(save_path, "ops.npy", 2))
+        print(f"No mROI data detected, planes found: {len(all_ops)}")
 
     try:
         zstats_file = get_volume_stats(all_ops, overwrite=True)
@@ -220,7 +224,7 @@ def run_volume(
             zstats_file, os.path.join(save_path, "mean_volume_signal.png")
         )
         # todo: why is suite2p not saving timings to ops.npy?
-        plot_execution_time(zstats_file, os.path.join(save_path, "execution_time.png"))
+        # plot_execution_time(zstats_file, os.path.join(save_path, "execution_time.png"))
 
         res_z = [
             load_planar_results(ops_path, z_plane=i)
@@ -429,6 +433,8 @@ def run_plane(
     >> output_ops = lsp.run_plane(input_files[0], save_path="D://data//outputs", keep_raw=True, keep_registered=True, force_reg=True, force_detect=True)
     """
     from mbo_utilities.array_types import MboRawArray
+    from mbo_utilities.lazy_array import imread, imwrite
+    from mbo_utilities.metadata import get_metadata
 
     if "debug" in kwargs:
         logger.setLevel(logging.DEBUG)
@@ -466,7 +472,7 @@ def run_plane(
             ops["diameter"]) > 1 and ops["aspect"] == 1.0:
         ops["aspect"] = ops["diameter"][0] / ops["diameter"][1]  # noqa
 
-    file = mbo.imread(input_path)
+    file = imread(input_path)
     if isinstance(file, MboRawArray):
         raise TypeError(
             "Input file appears to be a raw array. Please provide a planar input file."
@@ -474,7 +480,7 @@ def run_plane(
     if hasattr(file, "metadata"):
         metadata = file.metadata  # noqa
     else:
-        metadata = mbo.get_metadata(input_path)
+        metadata = get_metadata(input_path)
 
     if "plane" in ops:
         plane = ops["plane"]
@@ -484,7 +490,7 @@ def run_plane(
         ops["plane"] = plane
     else:
         # get the plane from the filename
-        plane = mbo.get_plane_from_filename(input_path, ops.get("plane", None))
+        plane = get_plane_from_filename(input_path, ops.get("plane", None))
         ops["plane"] = plane
         metadata["plane"] = plane
 
@@ -530,7 +536,7 @@ def run_plane(
 
     if _should_write_bin(ops_file, force=kwargs.get("force_save", False)):
         md_combined = {**metadata, **ops}
-        mbo.imwrite(file, plane_dir, ext=".bin", metadata=md_combined, register_z=False)
+        imwrite(file, plane_dir, ext=".bin", metadata=md_combined, register_z=False)
     else:
         print(
             f"Skipping data_raw.bin write, already exists and passes data validation checks."
@@ -600,7 +606,7 @@ def run_plane(
     save_pc_panels_and_metrics(ops_file, plane_dir / "pc_metrics")
 
     try:
-        remake_plane_figures(
+        plot_zplane_figures(
             plane_dir,
             dff_percentile=dff_percentile,
             dff_window_size=dff_window_size,