In Situ Hybridization

We have written pipelines using the freeware CellProfiler that can be used for the quantification of fluorescent in situ hybridization signals in both multiplex (RNAscope) and single-plex (BaseScope) modes. The published pipelines can be downloaded here  (scroll down to Erben L et al. 2017). Please cite this published work when using these pipelines, as indicated below: 

Erben L, He M-X, Laeremans A, Park E, Buonanno A (2017). A Novel Ultrasensitive In Situ Hybridization Approach to Detect Short Sequences and Splice Variants with Cellular Resolution. Mol Neurobiol. / doi . PMID: 29264769.

To run the pipeline, first download the current version  of CellProfiler. Older pipelines should be compatible with newer versions of CellProfiler.

If  CellProfiler is used in a publication, also remember to cite the original work as shown below.

Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, Guertin DA, Chang JH, Lindquist RA, Moffat J, Golland P, Sabatini DM (2006) CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biology 7:R100. /doi  PMID: 17076895