Connect the dots

3D "dot" tracking for pairs of tagged chromatin loci.

Basic installation instructions

There are a few dependencies that need to be installed before one can run connect_the_dots. These instructions are only for installation on our Ubuntu machines (tested for a clean installation of Ubuntu 18.04, July 23rd, 2020)

Please note that if any command below has the words sudo in them, it is likely you do not have to run them on our system. sudo means that the installation is system wide, therefore it usually only has to be done once by one user.

1. Install BioFormats

   • run git clone https://github.com/ome/bioformats into your desired folder
   • After downloading, install via the command line: run ant jars. If ant is not installed, run sudo apt-get install ant
   • https://docs.openmicroscopy.org/bio-formats/5.8.2/developers/building-bioformats.html#source-obtain-and-build

2. Install Java-Development-Kit

   • sudo apt install default-jdk
     • https://openjdk.java.net/install/

3. Install javabridge

   • IMPORTANT: Make sure you have correctly set the JAVA_HOME variable so that javabridge knows where to look for Java
   • For our system, this amounts to running in the command line: JAVA_HOME="/usr/lib/jvm/default-java/". For more details see issue here: LeeKamentsky/python-javabridge#152.
   • Boto3 is a required dependency, so run: pip install boto3
   • Finally, run pip install javabridge

4. Install python-bioformats from the people at CellProfiler

   • run pip install python-bioformats

5. Install tifffile

   • This is used to parse metadata
   • run pip install tifffile

6. Install ffmpeg (optional)

   • If this is not already installed on the system (i.e. if movies of trajectories are not saving)
   • run sudo apt install ffmpeg

7. Install Keras and Tensorflow2 (optional)

   • Install Tensorflow 2. Run pip install --upgrade tensorflow
   • Install Keras. Run pip install keras
   • For additional information, refer to (https://www.tensorflow.org/install)

8. Now, you should be all set!

   • run python setup.py develop, and you are ready to go!

Here's the API

See the docs for more information.

References (to cite)

- Bioformats: https://www.ncbi.nlm.nih.gov/pubmed/20513764