Bokeh-based jupyter-interface for Registering spatio-molecular data to related Microscopy images.
-
Sample HE images (Repository Folder):
-
Sample DAPI image (Repository Folder):
-
Sample Spatio-molecular data (Repository Folder):
BoReMi has modest resource requirements: On a Surface Pro 7 tablet (Intel Core i5-1035G4, 16GB memory) it runs smoothly and opens the Merfish mouse brain dataset with ~83,000 cells (subsampled to ~10,000 cells for visualisation) and images with ~100 MP in about two minutes for PNG images and in about 1 minute for JPEG images. Downsampling the number of displayed data points to ~10,000, while all data points are being processed, ensures lag-free interaction even with modest computational resources.
-
Notebooks: To set up BoReMi, two notebooks are provided in the
BoReMi directory
on the repository's main page:GUI.ipynb
andFunctions.ipynb
.GUI.ipynb
serves as a graphical user interface.Functions.ipynb
contains all the necessary functions.
-
Obtaining the notebooks: There are two methods to obtain the notebooks.
- Direct Download: Click on "Code" at the upper right corner of this repository and select "Download ZIP". Move the downloaded .zip file to the desired directory on your local machine/cluster and unpack it.
- Git Clone: Use the command
git clone https://github.com/jaspreetishar/BoReMi.git
to clone the repository and extract the notebooks onto your local machine/cluster.
-
Required Libraries/Packages/Extensions: Ensure you install the necessary libraries, packages, and extensions specified in the
environment.yml
file located on the repository's main page using the following guidelines.-
Navigate to the Project Directory
-
First, navigate to the root directory of the project. For example:
cd path/to/BoReMi
Replace
path/to/BoReMi
with the actual path to the cloned repository.
-
-
Create a New Virtual Environment and Install Dependencies
-
To avoid conflicts with existing versions of the required libraries/packages/extensions, it is recommended to create a new virtual environment. For instance, you can use Conda to create this environment and install all the dependencies specified in the
environment.yml
file using the following set of commands:conda env create -f environment.yml conda activate boremi_env python -m ipykernel install --user --name=boremi_env
The third command will allow you to select the boremi_env kernel when running Jupyter Lab.
-
-
Update Regularly
-
Periodically check for updates to the
environment.yml
file and update your virtual environment accordingly to stay compatible with the latest features and fixes:conda env update -f environment.yml
-
By following these steps, you will ensure that BoReMi runs smoothly without any library conflicts, improving user experience.
-
-
Accessing the GUI: To use BoReMi, open the
GUI.ipynb
file by typing the following in the terminal or an Anaconda command prompt:jupyter-lab path/to/BoReMi/BoReMi/GUI.ipynb
Replace
path/to/BoReMi/BoReMi/GUI.ipynb
with the actual path to theGUI.ipynb
file present in theBoReMi directory
of the cloned repository. -
BoReMi Usage: Follow the provided guidelines and instructions inside
GUI.ipynb
. Begin using the tool and explore its functionalities. -
Exit: To exit the virtual environment, type the following in the terminal or an Anaconda command prompt:
conda deactivate