Merge pull request #1 from murphygroup/v1.2

V1.2 create and use PyPI packages

README.md

@@ -1,14 +1,34 @@
 # 3DCellComposer - A Versatile Pipeline Utilizing 2D Cell Segmentation Methods for 3D Cell Segmentation
 Haoran Chen and Robert F. Murphy\
 Carnegie Mellon University\
-V1.1 Dec 14, 2023
+V1.2 February 7, 2024
 
-We introduce 3DCellComposer, a versatile, open-source software designed as a general solution for 3D cell segmentation. It allows users to choose any existing 2D segmentation model appropriate for their tissue or cell type(s) without requiring any additional training. Moreover, we have enhanced our CellSegmentationEvaluator quality evaluation tool to support 3D images. It allows users to compare and select the most suitable 2D segmentation models for 3D tasks, without the need for human annotations to assess performance.
+3DCellComposer is a versatile, open-source software designed as a general solution for 3D cell segmentation. It allows users to choose any existing 2D segmentation model appropriate for their tissue or cell type(s) without requiring any additional training. Moreover, we have enhanced our CellSegmentationEvaluator quality evaluation tool to support 3D images. It allows users to compare and select the most suitable 2D segmentation models for 3D tasks, without the need for human annotations to assess performance.
 
-Reference: Haoran Chen and Robert F. Murphy (2023) 3DCellComposer - A Versatile Pipeline Utilizing 2D Cell Segmentation Methods for 3D Cell Segmentation
+It is available as a full-featured GitHub repository, and as a python package on PyPi that provides a simplified implementation that uses just DeepCell as the 2D segmenter.
 
+Reference: Haoran Chen and Robert F. Murphy (2023) 3DCellComposer - A Versatile Pipeline Utilizing 2D Cell Segmentation Methods for 3D Cell Segmentation. Under review.
 
-## Manual
+## Using the PyPI package
+
+To use the package, 
+```bash
+pip install ThreeDCellComposer
+```
+
+Then import the function, 
+```bash
+from ThreeDCellComposer.ThreeDCellComposer import ThreeDCellComposer
+```
+
+To call the function
+```bash
+ThreeDCellComposer(image_path,nucleus_channel_marker_list,cytoplasm_channel_marker_list,membrane_channel_marker_list,segmentation_method)
+```
+Where the channel lists are lists of strings consisting of the names (not numbers) of the channels to be used for segmentation. Only 'deepcell' is supported as the segmentation_method by the PyPI package at this time.
+
+
+## Using the repository version
 
 ### Overview
 The `3DCellComposer` script processes multiplexed imaging data for cell segmentation. It requires specific inputs including the path to the image file and lists of markers for different cell components (nucleus, cytoplasm, and cell membrane). It also includes an optional input for specifying the 2D segmentation method(s) to be utilized.
@@ -71,5 +91,5 @@ In this command, the script processes the image located at `./data/3D_IMC_image.
 ## Contact
 
 Robert F. Murphy - murphy@cmu.edu\
-Haoran Chen - hrchen@cmu.edu
+Haoran Chen - haoran.chen@stjude.org