This repository contains example input data, including raw images, codebooks, parameters, and segmentation labels needed to run the FISH spatial transcriptomics pipeline tool PIPEFISH. The datasets contained are: in situ sequencing (ISS) of a whole coronal slice of a mouse brain (50 genes). Link to publication. Gataric, M., Park, J.S., Li, T., Vaskivskyi, V., Svedlund, J., Strell, C., Roberts, K., Nilsson, M., Yates, L.R., Bayraktar, O. and Gerstung, M., 2021. PoSTcode: Probabilistic image-based spatial transcriptomics decoder. bioRxiv, pp.2021-10. MERFISH of human U2-OS cell cultures (130 genes). Link to publication. Moffitt, J.R., Hao, J., Wang, G., Chen, K.H., Babcock, H.P. and Zhuang, X., 2016. High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization. Proceedings of the National Academy of Sciences, 113(39), pp.11046-11051. seqFISH of a developing mouse embryo (351 genes). Link to publication. Lohoff, T., Ghazanfar, S., Missarova, A., Koulena, N., Pierson, N., Griffiths, J.A., Bardot, E.S., Eng, C.H., Tyser, R.C.V., Argelaguet, R. and Guibentif, C., 2022. Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis. Nature biotechnology, 40(1), pp.74-85. In order to correctly format the inputs, run the prep_input.py script for the dataset you wish to run while in the same directory as the script. Memory requirements for each dataset: iss_mouse_brain - 3GB merfish_human_u2os - 7GB seqfish_mouse_embryo - 37GB