Merge 8cf90ca into 9b83046

Dockerfile

@@ -6,14 +6,14 @@ RUN apt-get update && apt-get install -y gcc
 WORKDIR /scripts
 
 # copy over the requirements.txt and install dependencies
-COPY setup.py requirements.txt /opt/segmentation/
-RUN pip install -r /opt/segmentation/requirements.txt
+COPY setup.py requirements.txt /opt/ark-analysis/
+RUN pip install -r /opt/ark-analysis/requirements.txt
 
 # copy the scripts over
-COPY segmentation /opt/segmentation/segmentation
+COPY ark /opt/ark-analysis/ark
 
 # Install the package via setup.py
-RUN pip install /opt/segmentation
+RUN pip install /opt/ark-analysis
 
 # jupyter notebook
 CMD ["jupyter", "notebook", "--ip=0.0.0.0", "--allow-root"]

README.md

@@ -1,18 +1,17 @@
-# Segmentation
-Toolbox for segmenting multiplexed imaging data
+# ark-analysis
+Toolbox for analyzing multiplexed imaging data
 
 ## Info
 
-This project contains a deepcell-preprocessing and deepcell-postprocessing notebook. The preprocessing notebook reformats imaging-data for deepcell's 'Multiplex' segmentation. The postprocessing notebook takes the output of deepcell and consolidates your imaging data into an xarray.
-
+This project contains code and example scripts for analyzing multiplexed imaging data
 ## To install the project:
 
 Open terminal and navigate to where you want the code stored.
 
 Then input the command:
 
 ```
-$ git clone https://github.com/angelolab/segmentation.git
+$ git clone https://github.com/angelolab/ark-analysis.git
 ```
 
 Next, you'll need to set up a docker image with all of the required dependencies.
@@ -21,8 +20,8 @@ Next, you'll need to set up a docker image with all of the required dependencies
  - Once it's running, enter the following commands into terminal 
 
 ```
-$ cd segmentation
-$ docker build -t segmentation .
+$ cd ark-analysis
+$ docker build -t ark-analysis .
 ``` 
 
 You've now installed the code base. 
@@ -39,6 +38,12 @@ This will generate a link to a jupyter notebook. Copy the last URL (the one with
 
 Be sure to keep this terminal open.  **Do not exit the terminal or enter control-c until you are finished with the notebooks**.
 
+## Using the example notebooks:
+- The Deepcell_preprocessing notebook walks you through the appropriate formatting steps in order to run your data through DeepCell to be segmented
+- The Deepcell_postprocessing notebooks takes the segmentation predictions from DeepCell, and uses them to extract the counts of each marker from your dataset
+- The spatial_analysis notebook contains code for performing cluster- and channel-based randomization, as well as neighborhood analysis. 
+
+
 ## Once you are finished
 
 You can shut down the notebooks and close docker by entering control-c in the terminal window.

start_docker.sh

@@ -30,7 +30,7 @@ fi
 
 docker run -it \
   -p 8888:8888 \
-  -v "$PWD/segmentation:/usr/local/lib/python3.6/site-packages/segmentation" \
+  -v "$PWD/ark:/usr/local/lib/python3.6/site-packages/ark" \
   -v "$PWD/scripts:/scripts" \
   -v "$PWD/data:/data" \
-  segmentation:latest
+  ark-analysis:latest