RAMFISH Software Suite
A comprehensive computational pipeline for multiplexed spatial biology. Handles signal normalization, image alignment, and LoG-based single-spot counting to generate accurate RNA profiles.
NEO-CRISPR
A dedicated computational tool and repository designed to facilitate and analyze precise CRISPR-based genome editing experiments.
HCR Probe Designer
A web-based tool for designing Hybridization Chain Reaction (HCR) probes. The app automates probe generation, amplifier selection, and sequence formatting for multiplexed spatial transcriptomics experiments.
HCR Probe Finder
Search the lab's HCR probe sets, or pick ready-designed probe pairs for any gene in Bicyclus anynana and zebrafish, including pairs for single splice variants. Choose B1, B2 or B3 and a fluorophore, then download an IDT-ready oPool sheet.
RGB based multiplex-FISH Probe Designer
A web-based tool for designing RGB style probes for detection of upto 6 genes using 3 amplifiers. This app helps you design probes for channel combinations for multiplexed spatial gene expression patterns.
RAMFISH Merger
A client-side web application for merging up to 30 single-channel RNAFISH images. Instantly generate highly multiplexed spatial composites with interactive controls for background thresholding, gamma correction, and dynamic legends.
RAMFISH Fine Aligner
A cloud-connected spatial biology tool for non-rigid image registration. It utilizes a B-Spline deformation framework to mathematically correct micro-scale tissue shifting, swelling, or mechanical warping across consecutive multiplexed RAM-FISH hybridization rounds.