FICT - FISH Iterative Cell Typing

is a package facilitates accurate cell clustering by iteratively incorporating neighborhood information using the Expectation-Maximization algorithm, designed for data generated through the Fluorescence in situ Hybridization (FISH) technique

Installation

git clone https://github.com/haotianteng/FICT.git
cd FICT
conda activate YOUR_VIR_ENVIRONMENT
python setup.py install
fict --help

Prepare dataset for running

Currently different FISH project using different data format, so 4 scripts are provided for dataset preparation for different datasets in FICT-SAMPLE tutorial repository.

Sample code

Please check FICT-SAMPLE for sample code to run FICT.

Citing FICT

If you used FICT in your work, please cite:

Teng, H., Yuan, Y., & Bar-Joseph, Z. (2021). Clustering Spatial Transcriptomics Data. Bioinformatics.

Issue report and contact

If you find any problem during using FICT, please don't hesitate to submit an issue through Github, or directly contact us through the email haotiant@andrew.cmu.edu