From e354b2fe6e5735c1e89f6fbaec74fa73db0e0bca Mon Sep 17 00:00:00 2001 From: Aaron Kanzer Date: Fri, 19 Jun 2026 18:32:17 -0400 Subject: [PATCH] Add Scigantic to open-microscopy software list Add Scigantic, an OME-Zarr (NGFF) based platform for scientific data discovery, to the software resource table in src/OM_Software.md. The searchable index (docs/entries.json) is regenerated automatically by the build-site workflow on push. --- src/OM_Software.md | 1 + 1 file changed, 1 insertion(+) diff --git a/src/OM_Software.md b/src/OM_Software.md index a14a322..cc0d157 100644 --- a/src/OM_Software.md +++ b/src/OM_Software.md @@ -64,6 +64,7 @@ | **Quantitative Phase Imaging Tools** | Various Tools to reconstruct brightfield images under varying illumination using inverse modeling and neural networks. Datasets. Lei Tian Lab. |[Website](https://sites.bu.edu/tianlab/open-source/), [GitHub](https://github.com/bu-cisl ) | **QuPath** | Open software platform especially for histopathology. |[Bankhead2017](https://doi.org/10.1038/s41598-017-17204-5), [GitHub](https://qupath.github.io/), | **Ray-optics web app** | An open-source web application to simulate reflection and refraction of light. | [GitHub/Website](https://ricktu288.github.io/ray-optics/) +| **Scigantic** | OME-Zarr (NGFF) native platform for scientific data discovery, enabling cloud-based storage, sharing and exploration of large bioimaging datasets directly in the OME-Zarr format. | [Website](https://scigantic.com) | **SMAP** | Open-source superresolution microscopy analysis platform. MATLAB-based tool with GUI to fit raw data, post-process and analyze SMLM data. Contains a powerful ROI manager and many other plugins, can be extended by own plugins (documentation available). Ries Lab. | [Ries2020](https://www.nature.com/articles/s41592-020-0938-1), [GitHub](https://github.com/jries/SMAP) | **StarDist** | Nuclei segmentation. | [Weigert2019](http://arxiv.org/abs/1908.03636), [GitHub](https://github.com/stardist/stardist) | **ThunderSTORM** |An open-source, interactive, and modular plug-in for ImageJ designed for automated processing, analysis, and visualization of data acquired by single molecule localization microscopy methods. |[Ovesný2014](https://doi.org/10.1093/bioinformatics/btu202), [GitHub](http://zitmen.github.io/thunderstorm/)