vizgen post processing tools (Vizgen Inc)

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Vizgen Inc vizgen post processing tools
Vizgen Post Processing Tools, supplied by Vizgen Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/post-processing+tool/post+processing+tool+vizgen/pmc12776951-286-9-9
Average 86 stars, based on 1 article reviews

vizgen post processing tools - by Bioz Stars, 2026-10

86/100 stars

Images

Imaging:

Article Title: Multimodal alignments of in vivo imaging and spatial biology datasets at cellular resolution
Article Snippet: .. We processed MERFISH imaging data by using the Vizgen Post-processing Tool (VPT, Vizgen) for cell segmentation and Vizualizer software (Vizgen) for data visualization and export. ..

Software:

Gene Expression:

Article Title: Logistic regression for estimating functional effects with spatial transcriptomics
Article Snippet: .. Vizgen Post-processing Tool output with CCFv3 registration is available as HDF5 files on the NIH Gene Expression Omnibus (GEO) at ncbi.nlm.nih.gov/geo/ , accession number GSE319949 . ..

Staining:

Article Title: SpatialBench : Comparative cross-platform benchmarking of high-resolution spatial transcriptomics using matched mouse lymphoid tissue
Article Snippet: .. For MERSCOPE datasets, segmentations and transcript-to-cell assignments were obtained using the Vizgen Post-Processing Tool (VPT v1.3.0) via the WEHI-SODA-Hub/spatialvpt pipeline (v1.0.0), which applies a Cellpose-based segmentation model to cell boundary (Cellbound), nuclear (DAPI), and cytoplasmic (Poly-T) staining channels. ..

Article Title: Single-cell spatial transcriptomic analysis of human skin anatomy.
Article Snippet: .. Segmentation was performed with the Vizgen postprocessing tool (VPT; v1.3)63 using Cellpose with DAPI and Cellbound3 stain (proprietary antibody cocktail stain manufactured by Vizgen) or DAPI alone for benchmarking comparisons64. ..

other:

Article Title: A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types.
Article Snippet: To gel-embed tissue samples on slides, a mix composed of Vizgen Gel Embedding Premix, ammonium persulfate (APS; Sigma: 09913-100G), and TEMED (Sigma: T7024-25ML) was prepared and applied to the tissue.

Generated:

Article Title: Identifying 3D signal overlaps in spatial transcriptomics data with ovrlpy.
Article Snippet: Imaging-based spatially resolved transcriptomics can localize transcripts within tissue sections in three dimensions.. However, cell segmentation, which assigns transcripts to cells, is usually performed in two dimensions and spatial doublets in the vertical dimension result in segmented cells containing transcripts originating from multiple cell types.. Here we present a computational tool called ovrlpy that identifies overlapping cells, tissue folds and inaccurate cell segmentation by analyzing transcript localization in three dimensions.

Review