version: release v1.0.0

Author: WenChentao

CellTracker/stardistwrapper.py

@@ -42,6 +42,11 @@ def load_stardist_model(model_name: str = "stardist", basedir: str = STARDIST_MO
     return model
 
 
+def imread_pillow(image_paths):
+    images = [np.asarray(Image.open(path)) for path in image_paths]
+    return np.stack(images, axis=0)
+
+
 def load_2d_slices_at_time(images_path: str | dict, t: int, do_normalize: bool = True):
     """Load all 2D slices at time t and normalize the resulted 3D image"""
     if isinstance(images_path, str):
@@ -50,7 +55,7 @@ def load_2d_slices_at_time(images_path: str | dict, t: int, do_normalize: bool =
         slice_paths_at_t = sorted(glob(images_path % t))
         if len(slice_paths_at_t) == 0:
             raise FileNotFoundError(f"No image at time {t} was found")
-        x = imread(slice_paths_at_t)
+        x = imread_pillow(slice_paths_at_t)
     elif isinstance(images_path, dict):
         file_extension = os.path.splitext(images_path["h5_file"])[1]
         assert file_extension in [".h5", ".hdf5"], "Currently only TIFF sequences or HDF5 dataset are supported"

LOG.MD

@@ -1,3 +1,10 @@
+### 2024.02.27
+3DeeCellTracker v1.0.0 has been released
+
+### 2023.04.24
+3DeeCellTracker v0.5.2-alpha has been released
+- fixed a potential bug related to matplotlib
+
 ### 2023.04.24
 3DeeCellTracker v0.5.1-alpha was released with following issues fixed
 - updated versions of some packages in the requirements.txt and setup.cfg

README.md

@@ -5,18 +5,8 @@
 **3DeeCellTracker** is a deep-learning based pipeline for tracking cells in 3D time-lapse images of deforming/moving organs ([eLife, 2021](https://elifesciences.org/articles/59187)).
 
 ## Updates:
-**3DeeCellTracker v0.5.2-alpha has been released**
-- fixed a potential bug related to matplotlib
-
-**3DeeCellTracker v0.5.1-alpha has been released**
-- Updated versions of some packages in requirements.txt and setup.cfg
-
-**3DeeCellTracker v0.5.0-alpha has been released**
-- Allows you to use [StarDist3D](https://github.com/stardist/stardist) for segmentation
-- Reduces the requirements for fine-tuning parameters
-- Decouples the code to facilitate reuse by third-party developers.
-
-
+**3DeeCellTracker v1.0.0 has been released**
+- Fixed some bugs in v0.5
 
 ## Installation
 
@@ -44,7 +34,7 @@ To install 3DeeCellTracker, please follow the instructions below:
 3. Install the 3DeeCellTracker package by running the following command in your terminal:
 
    ```console
-   $ pip install 3DeeCellTracker==0.5.2a0
+   $ pip install 3DeeCellTracker==1.0.0
    ```
 4. Once the installation is complete, you can start using 3DeeCellTracker for your 3D cell tracking tasks within the Jupyter notebooks provided in the GitHub repository.
 

setup.cfg

@@ -18,5 +18,6 @@ install_requires =
     stardist==0.8.3
     scikit-learn==1.1.2
     notebook==6.0.0
+    numpy~=1.19.5
 
 python_requires = >=3.6