Tools - FocalPlane

Displaying posts in the category: Tools

BioImaging North America- Builder's Workshop Series- Today- April 16

Posted by BioImaging North America, on 16 April 2026

Join BINA today for “Industry Involvement in Open-Hardware” featuring speakers from customScopes, ASI, Pacific Optica & Cephla.

Imaging spotlight: Minimally invasive live tissue clearing with SeeDB-Live

Posted by Takeshi Imai, on 1 April 2026

In this paper highlight from Shigenori Inagaki and Takeshi Imai, we learn about SeeDB-Live, a methodology for applying tissue clearing to live-cell imaging.

Back to the density: using Surface Morphometrics to measure organelle membrane thickness in cryo-electron tomography

Posted by Michaela Medina, on 18 March 2026

Surface Morphometrics is an open-access software that extracts quantitative information of membrane ultrastructure from high resolution cryo-electron tomography (cryo-ET) data. This tooling allows for the study of organelles in their native environment across large populations in an automated fashion. The Surface Morphometrics pipeline reconstructs three-dimensional triangular surface meshes to model and quantify the cellular membrane

Imaging spotlight: Altair-LSFM

Posted by FocalPlane, on 9 March 2026

In this paper highlight from Kevin Dean and colleagues, we learn about Altair-LSFM, a light-sheet fluorescence microscope that they designed so it can be built and operated in biology labs without needing a full-time optical engineer.

Imaging spotlight: PhotoFiTT

Posted by FocalPlane, on 2 March 2026

In this paper highlight, we learn about PhotoFiTT, a framework for measuring phototoxicity in live-cell fluorescence microscopy. Mario Del Rosario and Estibaliz Gómez-de-Mariscal, the co-first authors of PhotoFiTT answer our questions about their work.

Imaging spotlight: ShapeSpaceExplorer

Posted by FocalPlane, on 5 February 2026

In this paper highlight, we learn about ShapeSpaceExplorer, a tool for measuring cell shape of migrating cells, developed by Samuel Jefferyes, Anne Straube and colleagues.

JCS snapshot: Tracking coordinated cellular dynamics in time-lapse microscopy with ARCOS.px

Posted by FocalPlane, on 29 January 2026

In our latest JCS snapshot we hear from Maciej Dobrzyński, who, together with Benjamin Grädel and colleagues, developed ARCOS.px, a software tool to automatically identify and track coordinated dynamic cellular events in time-lapse microscopy movies.

Imaging spotlight: Lock-in-SIM

Posted by FocalPlane, on 8 January 2026

In this paper highlight from Wenjie Liu and colleagues, we learn about Lock-in-SIM, a new methodology for structured illumination microscopy.

Microscopy preprints: bioimage analysis

Posted by FocalPlane, on 29 December 2025

Here is a curated selection of preprints published (or updated) recently. In this post we focus specifically on bioimage analysis and data management.

Imaging spotlight: u-Segment3D

Posted by FocalPlane, on 11 December 2025

In this paper highlight, we learn about u-Segment3D, a software framework developed by Felix Zhou and Gaudenz Danuser and colleagues.

Write a Tools post

Create an account or log in to post your story on FocalPlane.

Featured categories

Microscopy-related articles from our journals

Toggle-Untoggle – a cell segmentation tool with an interactive user verification interface J Cell Sci 2025 138: jcs264154
The ratio of Wnt signaling activity to Sox2 transcription factor levels predicts neuromesodermal fate potential Development 2025 152: dev204661
The short isoform of Tango1 is dispensable for zebrafish survival but is required for skeletal patterning and integrity Biology Open 2025 14: bio062117

Microscopy-related preprint highlights

© 2026. The Company of Biologists Ltd | Registered Charity 277992
Registered in England and Wales | Company Limited by Guarantee No 514735
Registered office: Bidder Building, Station Road, Histon, Cambridge CB24 9LF, UK