diff --git a/.github/workflows/apple.yml b/.github/workflows/apple.yml
index 17fff68..4d609e5 100644
--- a/.github/workflows/apple.yml
+++ b/.github/workflows/apple.yml
@@ -8,8 +8,8 @@ run-name: ${{ github.actor }}::pytest pcdl library on mac os x; the latest pytho
 on:
   push:
     branches: ["master", "v3", "v4"]
-  pull_request:
-    branches: ["master", "v3", "v4"]
+  #pull_request:
+  #  branches: ["master", "v3", "v4"]
 
 jobs:
   build-macosx:
@@ -17,8 +17,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        #python-version: ["3.12"]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.13"]
+        #python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     env:
       PYTHONPATH: /Users/runner/work/physicelldataloader/physicelldataloader
@@ -33,7 +33,7 @@ jobs:
       run: |
         brew install ffmpeg imagemagick
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest aicsimageio anndata matplotlib numpy pandas requests scipy vtk
+        python -m pip install flake8 pytest anndata bioio matplotlib numpy pandas requests scipy vtk
         python -m pip install /Users/runner/work/physicelldataloader/physicelldataloader -v
         #if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: lint with flake8
@@ -45,4 +45,3 @@ jobs:
     - name: test with pytest
       run: |
         pytest
-
diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml
index 933d075..8f0aa06 100644
--- a/.github/workflows/linux.yml
+++ b/.github/workflows/linux.yml
@@ -8,8 +8,8 @@ run-name: ${{ github.actor }}::pytest pcdl library on linux os; all python3 vers
 on:
   push:
     branches: ["master", "v3", "v4"]
-  pull_request:
-    branches: ["master", "v3", "v4"]
+  #pull_request:
+  #  branches: ["master", "v3", "v4"]
 
 jobs:
   build-linux:
@@ -17,8 +17,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        #python-version: ["3.12"]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.13"]
+        #python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     env:
       PYTHONPATH: /home/runner/work/physicelldataloader/physicelldataloader
@@ -33,7 +33,7 @@ jobs:
       run: |
         sudo apt install ffmpeg imagemagick
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest aicsimageio anndata matplotlib numpy pandas requests scipy vtk
+        python -m pip install flake8 pytest anndata bioio matplotlib numpy pandas requests scipy vtk
         python -m pip install /home/runner/work/physicelldataloader/physicelldataloader -v
         #if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: lint with flake8
diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml
index e2fbe83..f464fcc 100644
--- a/.github/workflows/windows.yml
+++ b/.github/workflows/windows.yml
@@ -8,8 +8,8 @@ run-name: ${{ github.actor }}::pytest pcdl library on windows os; the latest pyt
 on:
   push:
     branches: ["master", "v3", "v4"]
-  pull_request:
-    branches: ["master", "v3", "v4"]
+  #pull_request:
+  #  branches: ["master", "v3", "v4"]
 
 jobs:
   build-windows:
@@ -17,8 +17,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        #python-version: ["3.12"]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.13"]
+        #python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     env:
       PYTHONPATH: D:\a\physicelldataloader\physicelldataloader
@@ -33,7 +33,7 @@ jobs:
       run: |
         choco install ffmpeg imagemagick
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest aicsimageio anndata matplotlib numpy pandas requests scipy vtk
+        python -m pip install flake8 pytest anndata bioio matplotlib numpy pandas requests scipy vtk
         python -m pip install D:\a\physicelldataloader\physicelldataloader -v
         #echo 'set PYTHONPATH=D:\a\physicelldataloader\physicelldataloader' >> $GITHUB_ENV
         #if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
diff --git a/README.md b/README.md
index 1dacc92..e884ad2 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,5 @@
 ![physicellcdataloader logo & title](man/img/physicelldataloader_title_v3.0.0.png)
 
-
 ## Abstract:
 
 physicelldataloader (pcdl) provides a platform independent, python3 based, [pip](https://en.wikipedia.org/wiki/Pip_(package_manager)) installable interface
@@ -20,7 +19,7 @@ The pcdl python3 library maintains three branches:
 ## Header:
 
 + Language: python [>= 3.9](https://devguide.python.org/versions/)
-+ Library dependencies: aicsimageio, anndata, matplotlib, numpy, pandas, (requests), scipy, vtk
++ Library dependencies: anndata, bioio, matplotlib, numpy, pandas, (requests), scipy, vtk
 + Date of origin original PhysiCell-Tools python-loader: 2019-09-02
 + Date of origin pcdl fork: 2022-08-30
 + Doi: https://doi.org/10.5281/ZENODO.8176399
@@ -123,10 +122,14 @@ Developers, please make pull requests to the https://github.com/elmbeech/physice
 
 + evt generate lineage tree graph output files.
 + evt add neuroglancer ome.tiff support.
-+ switch from aicsimageio to bioio library, when the library is ripe (napari has switched to bioio).
-
++ evt add DataDiVR support.
 
 ## Release Notes:
++ version 3.3.4 (2025-03-07): elmbeech/physicelldataloader
+    + replace the **aicsimageio** library dependency with its successor **bioio**. special thanks to Joel Eliason!
+    + **make_ome_tiff** can handle automatically generated file names with > 255 characters. special thank to Genevieve Stein-O'Brien and DanielBergman!
+    + **get_mesh_spacing** handels now an edge case correctly that would have resulted in a division by zero. special thanks to Randy Heiland!
+
 + version 3.3.3 (2025-01-10): elmbeech/physicelldataloader
     + bug fix **plot_contour** plot orientation. special thanks to Marco Ruscone!
     + add test data for new improved **unittest physicell model**. special thanks to Nick Oldfather!
diff --git a/man/TUTORIAL_blender.md b/man/TUTORIAL_blender.md
index fe53097..d5e05ca 100644
--- a/man/TUTORIAL_blender.md
+++ b/man/TUTORIAL_blender.md
@@ -66,25 +66,21 @@ To learn more about Blender and BVTK Node plugin, please study the official docu
 
 ## ✨ Handle ome tiff files
 
-The blender bioxel nodes plugin allows us load ome tiff files into blender.
+The blender bioxel nodes plugin allows us load single time step ome tiff files into blender.
 
-### Generate vtk files from the command line
+### Generate ome tiff files from the command line
 
 ```bash
-pcdl_make_conc_vtk output
-```
-```bash
-pcdl_make_cell_vtk output
+pcdl_make_ome_tiff output --collapse false
 ```
 
-### Generate vtk files from within python
+### Generate ome tiff files from within python
 
 ```python
 import pcdl
 
 mcdsts = pcdl.TimeSeries('output/')
-mcdsts.make_conc_vtk()
-mcdsts.make_cell_vtk()
+mcdsts.make_ome_tiff(collapse=False)
 ```
 
 ### The blender bioxel nodes plugin
diff --git a/man/TUTORIAL_python3_napari.md b/man/TUTORIAL_python3_napari.md
index 8dc3706..e6e6908 100644
--- a/man/TUTORIAL_python3_napari.md
+++ b/man/TUTORIAL_python3_napari.md
@@ -8,13 +8,8 @@ https://github.com/AllenCellModeling/napari-aicsimageio
 
 ## Install napari
 
-And install the [aicsimageio](https://github.com/AllenCellModeling/aicsimageio) library,
-which installs the "ome-types" napari plugin,
-that napari can read ome.tiff images inclusive ome metadata.
-
 ```bash
 pip3 install napari[all]
-pip3 install aicsimageio
 ```
 
 
diff --git a/man/TUTORIAL_python3_ometiff.md b/man/TUTORIAL_python3_ometiff.md
index abb3dd6..1274219 100644
--- a/man/TUTORIAL_python3_ometiff.md
+++ b/man/TUTORIAL_python3_ometiff.md
@@ -14,7 +14,7 @@ and [TUTORIAL_fiji_imagej.md](https://github.com/elmbeech/physicelldataloader/bl
 
 Additionally ome.tiff, tiff, png, and jpeg files can as well be loaded back in to python as [numpy](https://numpy.org/) array, for example with the [sci-kit image](https://scikit-image.org/) library (image data only).
 
-Besides that, ome.tiff files can be loaded with Allen Institute for Cell Science's [aicsimageio](https://github.com/AllenCellModeling/aicsimageio) library and possibly with its successor library [bioio](https://github.com/bioio-devs/bioio) (image and metadata).
+Besides that, ome.tiff files can be loaded with the [bioio](https://github.com/bioio-devs/bioio) library (image and metadata).
 
 
 ### Save pcdl data constructs from the command line into tiff and ome.tiff files
@@ -64,12 +64,12 @@ a_ome.shape  # (25, 2, 200, 300)
 ```
 
 
-### Load ome.tiff files as AICSImage object into python
+### Load ome.tiff files as BioImage object into python
 
 ```python
-from aicsimageio import AICSImage
+from bioio import BioImage
 
-img = AICSImage('output/timeseries_ID.ome.tiff')
+img = BioImage('output/timeseries_ID.ome.tiff')
 img.shape  # (25, 2, 1, 200, 300)
 ```
 ```python
diff --git a/pcdl/VERSION.py b/pcdl/VERSION.py
index bbeb48b..6c61f23 100644
--- a/pcdl/VERSION.py
+++ b/pcdl/VERSION.py
@@ -1 +1 @@
-__version__ = '3.3.3'
+__version__ = '3.3.4'
diff --git a/pcdl/ometiff2neuro.py b/pcdl/ometiff2neuro.py
new file mode 100644
index 0000000..5cb67aa
--- /dev/null
+++ b/pcdl/ometiff2neuro.py
@@ -0,0 +1,266 @@
+#########
+# title: ometiff2neuro.py
+#
+# language: python3
+# date: 2022-02-16
+# license: MIT
+# author: jason lu, viviana kwong, elmar bucher
+#
+# installation:
+#     conda create -n neuro python=3   # generate an own python environment for to run this code.
+#     conda activate neuro   # activate the generated python environment.
+#     pip install neuroglancer   # the basics
+#     pip install ipython   # for coding
+#     pip install matplotlib   # for expression value color maps
+#     pip install scikit-image   # for loading images as numpy array and signal thresh
+#     #pip install bioio   # for extracting ometiff metadata
+#
+# test dataset:
+#     conda activate neuro
+#     pip install synapseclient   # for downloading the test dataset from synapse
+#     synapse get -r syn26848775   # download test dataset into the current work directory folder.
+#
+# run:
+#     python3 -i ometiff2neuro.py <path/filename.tiff>
+#
+# description:
+#   script to render multi channel multi slice (ome)tiff files into the
+#   neuroglancer software.
+#
+#   the script here makes use of the neuroglancer python library and is based
+#   on the neuroglancer/python/examples/example.py code.
+#   with this script, it is possible to load three-dimensional single
+#   time step ome-tiff files straight into the neuroglancer software.
+#   for each channel, mesh generation, rendering, and expression intensity 
+#   coloring is done on the fly.
+#   channels can be viewed together or alone by toggling them on or off in
+#   the neuroglancer user interface.
+#
+# references:
+#   + https://www.openmicroscopy.org/ome-files/
+#   + https://github.com/google/neuroglancer
+#   + https://github.com/google/neuroglancer/tree/master/python
+#########
+
+
+# library
+import argparse
+from matplotlib import cm
+import neuroglancer
+import neuroglancer.cli
+import numpy as np
+from skimage import exposure, filters, io, util
+import sys
+
+
+# functions
+def ometiff2neuro(
+        o_state,
+        s_pathfile_tiff,
+        ls_channel_label = None, # ['DNA1','PD1','TLR3','SOX10', 'DNA2','CD163','CD3D','PDL1','DNA3','CD4','ICOS','HLADPB1','DNA4','CD8A','CD68','GZMB','DNA5','CD40L','LAG3','HLAA','DNA6','SQSTM','VIN','TIM3', 'DNA7','LAMP1/CD107A','PDL1_2','PD1_2', 'nuc_segement'], # dataset dependent information.
+        o_intensity_cm = cm.gray,  # None
+        b_intensity_norm = True,  # False
+        o_thresh = filters.threshold_li,  # None
+        di_coor = {'c':1, 'z':0, 'y':2, 'x':3},  # dataset dependent information.
+        di_nm = {'z':200, 'y':108, 'x':108},  # microscope dependent information.
+        e_render = None,  # {0, 'CD4', 'CD8A', 'GZMB', 28},
+    ):
+    '''
+    input:
+        o_state: neuroglancer viewer state object.
+
+        s_pathfile_tiff: file name and path to input tiff file.
+
+        ls_channel_label: list of channel labels.
+            default is None.
+            if None, hexadecimal channel labels will be generated.
+            this is dataset dependent information.
+            in future, if ometiff metadata is provided, this information will be extracted from the ometiff metadata.
+
+        o_intensity_cm: matlab color map object, used to display expression intensity values.
+            default is cm.gray.
+            if None, no intensity layers will be generated.
+
+        b_intensity_norm: boolean.
+            default is True.
+            if True, expression intensity values will be cut by the 2.5 and 97.5 percentiles, to remove outliers,
+                and intensity will be stretched over the whole range.
+
+        o_thresh: skimage.filter thresh method object to threshold non-threshed data.
+            default is filters.threshold_li.
+            this is dataset dependent information.
+            set None if the tiff contains no raw but already threshed or segmentation mask data!
+
+        di_coor: dictionary of integers, to link c,z,y, and x channel to the corresponding tiff (numpy array) columns.
+            this is dataset dependent information.
+            in future, if ometiff metadata is provided, this information will be extracted from the ometiff metadata.
+
+        di_nm: dictionary of integers, to specify z slice distance, and y x pixel size in nanometer.
+            this is microscope dependent information.
+            in future, if ometiff metadata is provided, this information will be extracted from the ometiff metadata.
+
+        e_render: set of channel marker labels and/or integers to specify which markers should be rendered into neurogalncer.
+            default is None.
+            if None, all channels will be rendered into neuroglancer (if enough RAM is available).
+
+    output:
+        local url where the rendered data can be viewed.
+
+    description:
+        function to render multi channel multi slice (ome)tiff files into the neuroglancer software.
+    '''
+    print(f'\nprocessing: {s_pathfile_tiff}')
+
+    # load tiff image as numpy array
+    a_img =  io.imread(s_pathfile_tiff)
+    print(f'image shape ({[m[0] for m in sorted(di_coor.items(), key=lambda n: n[1])]}): {a_img.shape}')
+
+    # channel count
+    i_channel = a_img.shape[di_coor['c']]
+
+    # handle channel labels
+    if ls_channel_label is None:
+        ls_channel_label = [hex(n) for n in range(i_channel)]
+    elif len(ls_channel_label) != i_channel:
+        sys.exit(f'Error @ ometiff2neuro : ls_channel_label shape (len(ls_channel_label)) does not match channel shape {i_channel}.')
+    print(f'ls_channel_label: {ls_channel_label}')
+
+    # handle set with labels from channels that will be rendered
+    if e_render is None:
+        e_render = set(range(i_channel))
+
+    # generate neuroglancer layers #
+    i_c = di_coor['c']
+    for i_n in range(i_channel):
+        s_label = ls_channel_label[i_n]
+        print(f'check channel {i_n}/{i_channel}: {s_label}')
+        if (i_n in e_render) or (s_label in e_render):
+            print(f'rendering channel {i_n}/{i_channel}: {s_label}')
+
+            # extract data and xyz coordinate columns
+            i_x = di_coor['x']
+            i_y = di_coor['y']
+            i_z = di_coor['z']
+            if i_c == 0:
+                a_channel = a_img[i_n,:,:,:]
+            elif i_c == 1:
+                a_channel = a_img[:,i_n,:,:]
+                if di_coor['x'] > i_c:
+                    i_x -= 1
+                if di_coor['y'] > i_c:
+                    i_y -= 1
+                if di_coor['z'] > i_c:
+                    i_z -= 1
+            elif i_c == 2:
+                a_channel = a_img[:,:,i_n,:]
+                if di_coor['x'] > i_c:
+                    i_x -= 1
+                if di_coor['y'] > i_c:
+                    i_y -= 1
+                if di_coor['z'] > i_c:
+                    i_z -= 1
+            elif i_c == 3:
+                a_channel = a_img[:,:,:,i_n]
+            else:
+                sys.exit(f'Error @ ometiff2neuro : the source code is broken. please, fix the script.')
+
+
+            # 3D rendering #
+            # thresh data
+            a_thresh = a_channel.copy()
+            if not (o_thresh is None):
+                r_thresh = o_thresh(a_thresh)
+                a_thresh[a_thresh < r_thresh] = 0
+            ab_thresh = a_thresh > 0
+
+            # shape
+            a_shape = np.zeros(ab_thresh.shape, dtype=np.uint32)
+            a_shape[ab_thresh] = i_n + 1
+
+            # generate neuroglancer object
+            ls_name = [None, None, None]
+            ls_name[i_x] = 'x'
+            ls_name[i_y] = 'y'
+            ls_name[i_z] = 'z'
+            li_scale = [None, None, None]
+            li_scale[i_x] = di_nm['x']
+            li_scale[i_y] = di_nm['y']
+            li_scale[i_z] = di_nm['z']
+            state.layers.append(
+                name = s_label,
+                layer = neuroglancer.LocalVolume(
+                    data = a_shape,
+                    dimensions = neuroglancer.CoordinateSpace(
+                        # rgb, x, y, z
+                        names = ls_name,
+                        scales = li_scale,
+                        units = ['nm', 'nm', 'nm'],
+                    ),
+                ),
+            )
+
+
+            # expression intensity rendering #
+            if not (o_intensity_cm is None):
+
+                # normalize expression values by clip by two sigma and scale over the whole uint range
+                if (b_intensity_norm):
+                    i_min_clip = int(np.percentile(a_channel, 2.5))
+                    i_max_clip = int(np.percentile(a_channel, 97.5))
+                    a_clipped = np.clip(a_channel, a_min=i_min_clip, a_max=i_max_clip)
+                    a_channel = exposure.rescale_intensity(a_clipped, in_range='image')  # 16 or 8[bit] normalized
+
+                # translate intensity by color map
+                a_8bit = util.img_as_ubyte(a_channel)
+                a_intensity = o_intensity_cm(a_8bit, alpha=None, bytes=True)[:,:,:,0:3]
+
+                # generate neuroglancer object
+                ls_name = [None, None, None,'c^']
+                ls_name[i_x] = 'x'
+                ls_name[i_y] = 'y'
+                ls_name[i_z] = 'z'
+                li_scale = [None, None, None, 3]
+                li_scale[i_x] = di_nm['x']
+                li_scale[i_y] = di_nm['y']
+                li_scale[i_z] = di_nm['z']
+                state.layers.append(
+                    name = s_label + '_intensity',
+                    layer = neuroglancer.LocalVolume(
+                        data = a_intensity,
+                        dimensions = neuroglancer.CoordinateSpace(
+                            # rgb, x, y, z
+                            names = ls_name,
+                            scales = li_scale,
+                            units = ['nm', 'nm', 'nm', ''],
+                        ),
+                    ),
+                    shader=
+"""
+void main() {
+  emitRGB(
+    vec3(toNormalized(getDataValue(0)),
+    toNormalized(getDataValue(1)),
+    toNormalized(getDataValue(2)))
+  );
+}
+""",
+            )
+
+
+# run the code from the command line
+if __name__ == '__main__':
+    o_parser = argparse.ArgumentParser(description='Script to render ome.tiff files into the neuroglancer software.')
+    # request path to ometiff and file name as command line argument
+    o_parser.add_argument('ometiff', type=str, nargs=1, help='ome.tiff path/filename')
+    # start neuroglancer
+    neuroglancer.cli.add_server_arguments(o_parser)
+    neuroglancer.cli.handle_server_arguments(o_parser.parse_args())
+    viewer = neuroglancer.Viewer()
+    with viewer.txn() as state:
+        # render ometiff
+        ometiff2neuro(
+            o_state = state,
+            s_pathfile_tiff = o_parser.parse_args().ometiff[0],
+        )
+    # print neuroglancer viewer url
+    print(viewer)
diff --git a/pcdl/pyCLI.py b/pcdl/pyCLI.py
index 41ad527..5a16608 100644
--- a/pcdl/pyCLI.py
+++ b/pcdl/pyCLI.py
@@ -1274,7 +1274,7 @@ def get_anndata():
         )
         # going home
         s_opathfile = s_pathfile.replace('.xml', f'_cell_{args.scale}.h5ad')
-        ann_mcds.write(s_opathfile)
+        ann_mcds.write_h5ad(s_opathfile)
         return s_opathfile
 
     else:
@@ -1300,12 +1300,12 @@ def get_anndata():
         # going home
         if b_collapse :
             s_opathfile = f'{s_path}/timeseries_cell_{args.scale}.h5ad'
-            ann_mcdsts.write(s_opathfile)
+            ann_mcdsts.write_h5ad(s_opathfile)
             return s_opathfile
         else:
             ls_opathfile = [f"{s_path}/{s_xmlfile.replace('.xml', '_cell_{}.h5ad'.format(args.scale))}" for s_xmlfile in mcdsts.get_xmlfile_list()]
             for i, ann_mcds in enumerate(ann_mcdsts):
-                ann_mcds.write(ls_opathfile[i])
+                ann_mcds.write_h5ad(ls_opathfile[i])
             return ls_opathfile
 
 
diff --git a/pcdl/pyMCDS.py b/pcdl/pyMCDS.py
index 1c1c33e..5a1fc2d 100644
--- a/pcdl/pyMCDS.py
+++ b/pcdl/pyMCDS.py
@@ -15,8 +15,8 @@
 
 
 # load library
-import aicsimageio  # bioio, bioio_base
-from aicsimageio.writers import OmeTiffWriter
+import bioio_base
+from bioio.writers import OmeTiffWriter
 import matplotlib.pyplot as plt
 from matplotlib import cm
 from matplotlib import colors
@@ -569,12 +569,22 @@ def get_mesh_spacing(self):
         tr_m_range, tr_n_range, tr_p_range = self.get_mesh_mnp_range()
         ar_m_axis, ar_n_axis, ar_p_axis = self.get_mesh_mnp_axis()
 
-        dm = (tr_m_range[1] - tr_m_range[0]) / (ar_m_axis.shape[0] - 1)
-        dn = (tr_n_range[1] - tr_n_range[0]) / (ar_n_axis.shape[0] - 1)
+        # m axis
+        if (len(set(tr_m_range)) == 1):
+            dm = np.float64(1.0)
+        else:
+            dm = (tr_m_range[1] - tr_m_range[0]) / (ar_m_axis.shape[0] - 1)
+        # n axis
+        if (len(set(tr_n_range)) == 1):
+            dn = np.float64(1.0)
+        else:
+            dn = (tr_n_range[1] - tr_n_range[0]) / (ar_n_axis.shape[0] - 1)
+        # p axis
         if (len(set(tr_p_range)) == 1):
             dp = np.float64(1.0)
         else:
             dp = (tr_p_range[1] - tr_p_range[0]) / (ar_p_axis.shape[0] - 1)
+
         return [dm, dn, dp]
 
 
@@ -1412,7 +1422,7 @@ def make_conc_vtk(self, visualize=True):
                 iren.Start()
 
             # free memory
-            del vfa_value
+            #del vfa_value
 
         # save vtk file
         s_vtkpathfile = self.path + '/' + s_vtkfile
@@ -2062,7 +2072,8 @@ def make_cell_vtk(self, attribute=['cell_type'], visualize=True):
                     voa_data.InsertNextValue(df_cell.loc[i, s_attribute])
 
             vug_data.GetPointData().AddArray(voa_data)
-            del voa_data
+            # free memory
+            #del voa_data
 
         # generate sphere source
         vss_data = vtk.vtkSphereSource()
@@ -2327,7 +2338,12 @@ def make_ome_tiff(self, cell_attribute='ID', conc_cutoff={}, focus=None, file=Tr
             if len(ls_celltype) > 0:
                 s_channel += f'_{cell_attribute}'
             s_tifffile = self.xmlfile.replace('.xml', f'{s_channel}.ome.tiff')
+            if (len(s_tifffile) > 255):
+                print(f"Warning: filename {len(s_tifffile)} > 255 character.")
+                s_tifffile = self.xmlfile.replace('.xml', f'_channels.ome.tiff')
+                print(f"file name adjusted to {s_tifffile}.")
             s_tiffpathfile = self.path + '/' + s_tifffile
+
             # save to file
             OmeTiffWriter.save(
                 a_czyx_img,
@@ -2336,7 +2352,7 @@ def make_ome_tiff(self, cell_attribute='ID', conc_cutoff={}, focus=None, file=Tr
                 #ome_xml=x_img,
                 channel_names = ls_channel,
                 image_names = [s_tifffile.replace('.ome.tiff','')],
-                physical_pixel_sizes = aicsimageio.types.PhysicalPixelSizes(self.get_voxel_spacing()[2], 1.0, 1.0),  # z,y,x [um]
+                physical_pixel_sizes = bioio_base.types.PhysicalPixelSizes(self.get_voxel_spacing()[2], 1.0, 1.0),  # z,y,x [um]
                 #channel_colors=,
                 #fs_kwargs={},
             )
diff --git a/pcdl/pyMCDSts.py b/pcdl/pyMCDSts.py
index 0ff04ba..2378a38 100644
--- a/pcdl/pyMCDSts.py
+++ b/pcdl/pyMCDSts.py
@@ -20,8 +20,8 @@
 
 
 # load libraries
-import aicsimageio  # bioio, bioio_base
-from aicsimageio.writers import OmeTiffWriter
+import bioio_base
+from bioio.writers import OmeTiffWriter
 import glob
 import matplotlib.pyplot as plt
 import numpy as np
@@ -1082,6 +1082,7 @@ def make_ome_tiff(self, cell_attribute='ID', conc_cutoff={}, focus=None, file=Tr
             a_tczyx_img = np.array(l_tczyx_img)
             if self.verbose:
                 print('a_tczyx_img shape:', a_tczyx_img.shape)
+
             # generate filename
             s_channel = ''
             for s_substrate in ls_substrate:
@@ -1094,7 +1095,13 @@ def make_ome_tiff(self, cell_attribute='ID', conc_cutoff={}, focus=None, file=Tr
                 s_channel += f'_{s_celltype}'
             if len(ls_celltype) > 0:
                 s_channel += f'_{cell_attribute}'
-            s_tiffpathfile = self.path + f'/timeseries{s_channel}.ome.tiff'
+            s_tifffile = f'timeseries{s_channel}.ome.tiff'
+            if (len(s_tifffile) > 255):
+                print(f"Warning: filename {len(s_tifffile)} > 255 character.")
+                s_tifffile = 'timeseries_channels.ome.tiff'
+                print(f"file name adjusted to {s_tifffile}.")
+            s_tiffpathfile = self.path + '/' + s_tifffile
+
             # save to file
             OmeTiffWriter.save(
                 a_tczyx_img,
@@ -1103,7 +1110,7 @@ def make_ome_tiff(self, cell_attribute='ID', conc_cutoff={}, focus=None, file=Tr
                 #ome_xml=x_img,
                 channel_names = ls_substrate + ls_celltype,
                 image_names = [f'timeseries_{cell_attribute}'],
-                physical_pixel_sizes = aicsimageio.types.PhysicalPixelSizes(mcds.get_voxel_spacing()[2], 1.0, 1.0),  # z,y,x [um]
+                physical_pixel_sizes = bioio_base.types.PhysicalPixelSizes(mcds.get_voxel_spacing()[2], 1.0, 1.0),  # z,y,x [um]
                 #channel_colors=,
                 #fs_kwargs={},
             )
diff --git a/pyproject.toml b/pyproject.toml
index a9048d2..1d21b09 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -70,8 +70,8 @@ classifiers = [
 
 # bue 2024-12-06: enforcing some versions
 dependencies = [
-    "aicsimageio",
     "anndata>=0.10.8",
+    "bioio>=1.2.1",
     "matplotlib",
     "numpy<2.0.0",
     "pandas>=2.2.2",
diff --git a/test/test_cli_2d.py b/test/test_cli_2d.py
index dded686..71b6aed 100644
--- a/test/test_cli_2d.py
+++ b/test/test_cli_2d.py
@@ -813,7 +813,7 @@ def test_pcdl_get_anndata_timeseries(self):
         s_result = subprocess.run(['pcdl_get_anndata', s_path_2d], check=False, capture_output=True)
         #print(f'\ns_result.stdout: {s_result.stdout}\n')
         #print(f'\ns_result.stderr: {s_result.stderr}\n')
-        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','')
+        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','').replace('<sys>:0:','sys:1:').replace('sys:1: DeprecationWarning: Call to deprecated function (or staticmethod) _destroy.','')  # bue 20250307: >= python3.11
         ann = ad.read_h5ad(s_opathfile)
         assert (s_opathfile.endswith('output_2d/timeseries_cell_maxabs.h5ad')) and \
                (ann.shape[0] >  9) and \
@@ -829,7 +829,7 @@ def test_pcdl_get_anndata_timeseries_collapsed(self):
         s_result = subprocess.run(['pcdl_get_anndata', s_path_2d, '--collapse', 'false'], check=False, capture_output=True)
         #print(f'\ns_result.stdout: {s_result.stdout}\n')
         #print(f'\ns_result.stderr: {s_result.stderr}\n')
-        ls_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace("['","").replace("']\n","").split("', '")
+        ls_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('<sys>:0:','sys:1:').replace('sys:1: DeprecationWarning: Call to deprecated function (or staticmethod) _destroy.\n','').replace("['","").replace("']\n","").split("', '")  # bue 20250307: >= python3.11
         assert len(ls_opathfile) == 25 and \
                ls_opathfile[0].endswith('output_2d/output00000000_cell_maxabs.h5ad') and \
                ls_opathfile[-1].endswith('output_2d/output00000024_cell_maxabs.h5ad') and \
@@ -841,7 +841,7 @@ def test_pcdl_get_anndata_timeseries_customtype(self):
         s_result = subprocess.run(['pcdl_get_anndata', s_path_2d, '--custom_data_type', 'sample:bool'], check=False, capture_output=True)
         #print(f'\ns_result.stdout: {s_result.stdout}\n')
         print(f'\ns_result.stderr: {s_result.stderr}\n')
-        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','')
+        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','').replace('<sys>:0:','sys:1:').replace('sys:1: DeprecationWarning: Call to deprecated function (or staticmethod) _destroy.','')  # bue 20250307: >= python3.11
         ann = ad.read_h5ad(s_opathfile)
         assert (s_opathfile.endswith('output_2d/timeseries_cell_maxabs.h5ad')) and \
                (set(ann.var_names).issuperset({'sample'})) and \
@@ -858,7 +858,7 @@ def test_pcdl_get_anndata_timeseries_microenv(self):
         s_result = subprocess.run(['pcdl_get_anndata', s_path_2d, '--microenv', 'false'], check=False, capture_output=True)
         #print(f'\ns_result.stdout: {s_result.stdout}\n')
         #print(f'\ns_result.stderr: {s_result.stderr}\n')
-        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','')
+        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','').replace('<sys>:0:','sys:1:').replace('sys:1: DeprecationWarning: Call to deprecated function (or staticmethod) _destroy.','')  # bue 20250307: >= python3.11
         ann = ad.read_h5ad(s_opathfile)
         assert (s_opathfile.endswith('output_2d/timeseries_cell_maxabs.h5ad')) and \
                (not set(ann.var_names).issuperset({'oxygen'})) and \
@@ -875,7 +875,7 @@ def test_pcdl_get_anndata_timeseries_graph(self):
         s_result = subprocess.run(['pcdl_get_anndata', s_path_2d, '--graph', 'false'], check=False, capture_output=True)
         #print(f'\ns_result.stdout: {s_result.stdout}\n')
         #print(f'\ns_result.stderr: {s_result.stderr}\n')
-        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','')
+        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','').replace('<sys>:0:','sys:1:').replace('sys:1: DeprecationWarning: Call to deprecated function (or staticmethod) _destroy.','')  # bue 20250307: >= python3.11
         ann = ad.read_h5ad(s_opathfile)
         assert (s_opathfile.endswith('output_2d/timeseries_cell_maxabs.h5ad')) and \
                (ann.shape[0] > 9) and \
@@ -891,7 +891,7 @@ def test_pcdl_get_anndata_timeseries_physiboss(self):
         s_result = subprocess.run(['pcdl_get_anndata', s_path_2d, '--physiboss', 'false'], check=False, capture_output=True)
         #print(f'\ns_result.stdout: {s_result.stdout}\n')
         #print(f'\ns_result.stderr: {s_result.stderr}\n')
-        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','')
+        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','').replace('<sys>:0:','sys:1:').replace('sys:1: DeprecationWarning: Call to deprecated function (or staticmethod) _destroy.','')  # bue 20250307: >= python3.11
         ann = ad.read_h5ad(s_opathfile)
         assert (s_opathfile.endswith('output_2d/timeseries_cell_maxabs.h5ad')) and \
                (ann.shape[0] > 9) and \
@@ -907,7 +907,7 @@ def test_pcdl_get_anndata_timeseries_settingxmlfalse(self):
         s_result = subprocess.run(['pcdl_get_anndata', s_path_2d, '--settingxml', 'false'], check=False, capture_output=True)
         #print(f'\ns_result.stdout: {s_result.stdout}\n')
         #print(f'\ns_result.stderr: {s_result.stderr}\n')
-        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','')
+        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','').replace('<sys>:0:','sys:1:').replace('sys:1: DeprecationWarning: Call to deprecated function (or staticmethod) _destroy.','')  # bue 20250307: >= python3.11
         ann = ad.read_h5ad(s_opathfile)
         assert (s_opathfile.endswith('output_2d/timeseries_cell_maxabs.h5ad')) and \
                (set(ann.var_names).issuperset({'default_fusion_rates'})) and \
@@ -924,7 +924,7 @@ def test_pcdl_get_anndata_timeseries_settingxmlnone(self):
         s_result = subprocess.run(['pcdl_get_anndata', s_path_2d, '--settingxml', 'none'], check=False, capture_output=True)
         #print(f'\ns_result.stdout: {s_result.stdout}\n')
         #print(f'\ns_result.stderr: {s_result.stderr}\n')
-        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','')
+        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','').replace('<sys>:0:','sys:1:').replace('sys:1: DeprecationWarning: Call to deprecated function (or staticmethod) _destroy.','')  # bue 20250307: >= python3.11
         ann = ad.read_h5ad(s_opathfile)
         assert (s_opathfile.endswith('output_2d/timeseries_cell_maxabs.h5ad')) and \
                (set(ann.var_names).issuperset({'default_fusion_rates'})) and \
@@ -941,7 +941,7 @@ def test_pcdl_get_anndata_timeseries_value(self):
         s_result = subprocess.run(['pcdl_get_anndata', s_path_2d, '2'], check=False, capture_output=True)
         #print(f'\ns_result.stdout: {s_result.stdout}\n')
         #print(f'\ns_result.stderr: {s_result.stderr}\n')
-        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','')
+        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','').replace('<sys>:0:','sys:1:').replace('sys:1: DeprecationWarning: Call to deprecated function (or staticmethod) _destroy.','')  # bue 20250307: >= python3.11
         ann = ad.read_h5ad(s_opathfile)
         assert (s_opathfile.endswith('output_2d/timeseries_cell_maxabs.h5ad')) and \
                (ann.shape[0] > 9) and \
@@ -957,7 +957,7 @@ def test_pcdl_get_anndata_timeseries_drop(self):
         s_result = subprocess.run(['pcdl_get_anndata', s_path_2d, '--drop', 'cell_type', 'oxygen'], check=False, capture_output=True)
         #print(f'\ns_result.stdout: {s_result.stdout}\n')
         #print(f'\ns_result.stderr: {s_result.stderr}\n')
-        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','')
+        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','').replace('<sys>:0:','sys:1:').replace('sys:1: DeprecationWarning: Call to deprecated function (or staticmethod) _destroy.','')  # bue 20250307: >= python3.11
         ann = ad.read_h5ad(s_opathfile)
         assert (s_opathfile.endswith('output_2d/timeseries_cell_maxabs.h5ad')) and \
                (not set(ann.var_names).issuperset({'cell_type'})) and \
@@ -975,7 +975,7 @@ def test_pcdl_get_anndata_timeseries_keep(self):
         s_result = subprocess.run(['pcdl_get_anndata', s_path_2d, '--keep', 'cell_type', 'oxygen'], check=False, capture_output=True)
         #print(f'\ns_result.stdout: {s_result.stdout}\n')
         #print(f'\ns_result.stderr: {s_result.stderr}\n')
-        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','')
+        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','').replace('<sys>:0:','sys:1:').replace('sys:1: DeprecationWarning: Call to deprecated function (or staticmethod) _destroy.','')  # bue 20250307: >= python3.11
         ann = ad.read_h5ad(s_opathfile)
         assert (s_opathfile.endswith('output_2d/timeseries_cell_maxabs.h5ad')) and \
                (set(ann.var_names).issuperset({'oxygen'})) and \
@@ -993,7 +993,7 @@ def test_pcdl_get_anndata_timeseries_scale(self):
         s_result = subprocess.run(['pcdl_get_anndata', s_path_2d, '--scale', 'std'], check=False, capture_output=True)
         #print(f'\ns_result.stdout: {s_result.stdout}\n')
         #print(f'\ns_result.stderr: {s_result.stderr}\n')
-        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','')
+        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','').replace('<sys>:0:','sys:1:').replace('sys:1: DeprecationWarning: Call to deprecated function (or staticmethod) _destroy.','')  # bue 20250307: >= python3.11
         ann = ad.read_h5ad(s_opathfile)
         assert (s_opathfile.endswith('output_2d/timeseries_cell_std.h5ad')) and \
                (ann.shape[0] > 9) and \
@@ -1010,7 +1010,7 @@ def test_pcdl_get_anndata_timestep(self):
         s_result = subprocess.run(['pcdl_get_anndata', s_pathfile_2d], check=False, capture_output=True)
         #print(f'\ns_result.stdout: {s_result.stdout}\n')
         #print(f'\ns_result.stderr: {s_result.stderr}\n')
-        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','')
+        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','').replace('<sys>:0:','sys:1:').replace('sys:1: DeprecationWarning: Call to deprecated function (or staticmethod) _destroy.','')  # bue 20250307: >= python3.11
         ann = ad.read_h5ad(s_opathfile)
         assert (s_opathfile.endswith('output_2d/output00000024_cell_maxabs.h5ad')) and \
                (ann.shape[0] > 9) and \
@@ -1026,7 +1026,7 @@ def test_pcdl_get_anndata_timestep_microenv(self):
         s_result = subprocess.run(['pcdl_get_anndata', s_pathfile_2d, '--microenv', 'false'], check=False, capture_output=True)
         #print(f'\ns_result.stdout: {s_result.stdout}\n')
         #print(f'\ns_result.stderr: {s_result.stderr}\n')
-        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','')
+        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','').replace('<sys>:0:','sys:1:').replace('sys:1: DeprecationWarning: Call to deprecated function (or staticmethod) _destroy.','')  # bue 20250307: >= python3.11
         ann = ad.read_h5ad(s_opathfile)
         assert (s_opathfile.endswith('output_2d/output00000024_cell_maxabs.h5ad')) and \
                (not set(ann.var_names).issuperset({'oxygen'})) and \
@@ -1043,7 +1043,7 @@ def test_pcdl_get_anndata_timestep_graph(self):
         s_result = subprocess.run(['pcdl_get_anndata', s_pathfile_2d, '--graph', 'false'], check=False, capture_output=True)
         #print(f'\ns_result.stdout: {s_result.stdout}\n')
         #print(f'\ns_result.stderr: {s_result.stderr}\n')
-        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','')
+        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','').replace('<sys>:0:','sys:1:').replace('sys:1: DeprecationWarning: Call to deprecated function (or staticmethod) _destroy.','')  # bue 20250307: >= python3.11
         ann = ad.read_h5ad(s_opathfile)
         assert (s_opathfile.endswith('output_2d/output00000024_cell_maxabs.h5ad')) and \
                (ann.shape[0] > 9) and \
@@ -1059,7 +1059,7 @@ def test_pcdl_get_anndata_timestep_physiboss(self):
         s_result = subprocess.run(['pcdl_get_anndata', s_pathfile_2d, '--physiboss', 'false'], check=False, capture_output=True)
         #print(f'\ns_result.stdout: {s_result.stdout}\n')
         #print(f'\ns_result.stderr: {s_result.stderr}\n')
-        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','')
+        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','').replace('<sys>:0:','sys:1:').replace('sys:1: DeprecationWarning: Call to deprecated function (or staticmethod) _destroy.','')  # bue 20250307: >= python3.11
         ann = ad.read_h5ad(s_opathfile)
         assert (s_opathfile.endswith('output_2d/output00000024_cell_maxabs.h5ad')) and \
                (ann.shape[0] > 9) and \
@@ -1075,7 +1075,7 @@ def test_pcdl_get_anndata_timestep_settingxmlfalse(self):
         s_result = subprocess.run(['pcdl_get_anndata', s_pathfile_2d, '--settingxml', 'false'], check=False, capture_output=True)
         #print(f'\ns_result.stdout: {s_result.stdout}\n')
         #print(f'\ns_result.stderr: {s_result.stderr}\n')
-        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','')
+        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','').replace('<sys>:0:','sys:1:').replace('sys:1: DeprecationWarning: Call to deprecated function (or staticmethod) _destroy.','')  # bue 20250307: >= python3.11
         ann = ad.read_h5ad(s_opathfile)
         assert (s_opathfile.endswith('output_2d/output00000024_cell_maxabs.h5ad')) and \
                (set(ann.var_names).issuperset({'default_fusion_rates'})) and \
@@ -1092,7 +1092,7 @@ def test_pcdl_get_anndata_timestep_settingxmlnone(self):
         s_result = subprocess.run(['pcdl_get_anndata', s_pathfile_2d, '--settingxml', 'none'], check=False, capture_output=True)
         #print(f'\ns_result.stdout: {s_result.stdout}\n')
         #print(f'\ns_result.stderr: {s_result.stderr}\n')
-        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','')
+        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','').replace('<sys>:0:','sys:1:').replace('sys:1: DeprecationWarning: Call to deprecated function (or staticmethod) _destroy.','')  # bue 20250307: >= python3.11
         ann = ad.read_h5ad(s_opathfile)
         assert (s_opathfile.endswith('output_2d/output00000024_cell_maxabs.h5ad')) and \
                (set(ann.var_names).issuperset({'default_fusion_rates'})) and \
@@ -1109,7 +1109,7 @@ def test_pcdl_get_anndata_timestep_value(self):
         s_result = subprocess.run(['pcdl_get_anndata', s_pathfile_2d, '2'], check=False, capture_output=True)
         #print(f'\ns_result.stdout: {s_result.stdout}\n')
         #print(f'\ns_result.stderr: {s_result.stderr}\n')
-        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','')
+        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','').replace('<sys>:0:','sys:1:').replace('sys:1: DeprecationWarning: Call to deprecated function (or staticmethod) _destroy.','')  # bue 20250307: >= python3.11
         ann = ad.read_h5ad(s_opathfile)
         assert (s_opathfile.endswith('output_2d/output00000024_cell_maxabs.h5ad')) and \
                (ann.shape[0] > 9) and \
@@ -1125,7 +1125,7 @@ def test_pcdl_get_anndata_timestep_drop(self):
         s_result = subprocess.run(['pcdl_get_anndata', s_pathfile_2d, '--drop', 'cell_type', 'oxygen'], check=False, capture_output=True)
         #print(f'\ns_result.stdout: {s_result.stdout}\n')
         #print(f'\ns_result.stderr: {s_result.stderr}\n')
-        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','')
+        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','').replace('<sys>:0:','sys:1:').replace('sys:1: DeprecationWarning: Call to deprecated function (or staticmethod) _destroy.','')  # bue 20250307: >= python3.11
         ann = ad.read_h5ad(s_opathfile)
         assert (s_opathfile.endswith('output_2d/output00000024_cell_maxabs.h5ad')) and \
                (not set(ann.var_names).issuperset({'cell_type'})) and \
@@ -1143,7 +1143,7 @@ def test_pcdl_get_anndata_timestep_keep(self):
         s_result = subprocess.run(['pcdl_get_anndata', s_pathfile_2d, '--keep', 'cell_type', 'oxygen'], check=False, capture_output=True)
         #print(f'\ns_result.stdout: {s_result.stdout}\n')
         #print(f'\ns_result.stderr: {s_result.stderr}\n')
-        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','')
+        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','').replace('<sys>:0:','sys:1:').replace('sys:1: DeprecationWarning: Call to deprecated function (or staticmethod) _destroy.','')  # bue 20250307: >= python3.11
         ann = ad.read_h5ad(s_opathfile)
         assert (s_opathfile.endswith('output_2d/output00000024_cell_maxabs.h5ad')) and \
                (set(ann.var_names).issuperset({'oxygen'})) and \
@@ -1161,7 +1161,7 @@ def test_pcdl_get_anndata_timestep_scale(self):
         s_result = subprocess.run(['pcdl_get_anndata', s_pathfile_2d, '--scale', 'std'], check=False, capture_output=True)
         #print(f'\ns_result.stdout: {s_result.stdout}\n')
         #print(f'\ns_result.stderr: {s_result.stderr}\n')
-        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','')
+        s_opathfile = s_result.stderr.decode('UTF8').replace('\r','').replace('\n','').replace('<sys>:0:','sys:1:').replace('sys:1: DeprecationWarning: Call to deprecated function (or staticmethod) _destroy.','')  # bue 20250307: >= python3.11
         ann = ad.read_h5ad(s_opathfile)
         assert (s_opathfile.endswith('output_2d/output00000024_cell_std.h5ad')) and \
                (ann.shape[0] > 9) and \