Installation

1. Navigate to the Loki2 source directory and create a conda environment:

   cd ./src
   conda env create -f environment.yaml
   conda activate loki2_env
   

2. Install Loki2:

   python -m pip install .
   

3. (Morphology-to-transcriptome retrieval only) create the OmiCLIP environment:

   Transcriptome encoding is done with OmiCLIP, the visual-omics foundation model behind Loki (Nature Methods). It ships its own environment, loki_env, which is separate from loki2_env and is only needed for encode_trans.py; every other step runs in loki2_env.

   Follow the installation instructions of the Loki repository:

   conda create -n loki_env python=3.9
   conda activate loki_env
   cd /path/to/Loki/src
   python -m pip install .
   

   Then download the OmiCLIP checkpoint omiclip.pt and place it in ./src/loki2/.