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Stephan Preibisch Profile picture
Stephan Preibisch
@preibischs
Open Science Software Enthusiast - Director of Scientific Computing & Team Leader Computational Method Development at HHMI Janelia
Dec 8, 2021 • 9 tweets • 5 min read
We (together with @nu_karaiskos & @N_Rajewsky) are excited to announce the open-source Spatial Transcriptomics Imaging Project (STIM). Its goal is to bring the worlds of transcriptomics and imaging together [1/8].

biorxiv.org/content/10.110… STIM is a computational framework for storing, exploring, visualizing, and processing of 2D & 3D spatial sequencing datasets that scales to large and high-throughput datasets [2/8].
Mar 10, 2021 • 8 tweets • 6 min read
We are excited to share with you RS-FISH: Precise, interactive and scalable smFISH spot detection in @FijiSc using 3D Radial Symmetry:

biorxiv.org/content/10.110…

(1/8) Max intensity projection of... Radial Symmetry (RS) localizes single, circular, two-dimensional spots by computing the intersection point of image gradients. For RS-FISH, we extended RS to detect smFISH spots in anisotropic 3D image datasets. (2/8) Image