tllab-common 2024.5.0

Common code for the Lenstra lab.

Common Code

Code that both LiveCellAnalysis and smFISH (or others) use and doesn't get major changes goes here. This code should be a submodule in smFISH and LiveCellAnalysis.

Command line tools:

wimread

wimread imagefile

Displays information (pixel size, interval time etc.) about the image file.

Installation (Ubuntu)

python-javabridge is required, which requires java, for ubuntu:

sudo apt install openjdk-8-jdk-headless

Set java 8 as default java:

sudo update-alternatives --config java

Then this code can be installed as a package:

pip install tllab_common

or editable:

git clone [e-mail]:Lenstralab/tllab_common.git
pip install -e tllab_common/ --user