EcClemv2: A new version of a flexible software for correlative workflows

Wednesday. August 25, 2021

Perrine Paul-Gilloteaux

Université de Nantes, CNRS, INSERM, l’institut du thorax; SFR Santé François Bonamy MicroPICell

Abstract

Accurate registration of imaging modalities is one of the key steps of a correlative imaging workflow. EcClem (1) is a plugin under the free and open source software plateform ICY (2) aiming to ease the registration process in correlative microscopies workflows, whatever the modalities in use. We present here a new version of EcClem and EcClemAutofinder, which is considerably faster and offer new tools to construct your own workflows. In particular, a full workflow can be constructed by taking into account several intermediate imaging steps to ease the correlation, which can be cascaded and automatized as a visual protocol under ICY. We also provide a new method of error estimation in registration, allowing to assess the co-localization of pixels from different registered modalities (3). New functionalities for the visualization of correlation are also presented. This new version of the software has already been used in correlative workflows by collaborators (4–6)

References:

1. Paul-Gilloteaux P, Heiligenstein X, Belle M, Domart M-C, Larijani B, Collinson L, et al. eC-CLEM: flexible multidimensional registration software for correlative microscopies. Nat Methods. févr 2017;14(2):102 3.

2. de Chaumont F, Dallongeville S, Chenouard N, Hervé N, Pop S, Provoost T, et al. Icy: an open bioimage informatics platform for extended reproducible research. Nat Methods. juill 2012;9(7):690 6.

3. Potier G, Lavancier F, Kunne S, Paul-Gilloteaux P. A registration error estimation framework for correlative imaging. ArXiv210306256 Cs Q-Bio [Internet]. 10 mars 2021 [cité 17 mars 2021]; Disponible sur: http://arxiv.org/abs/2103.06256

4. Scher N, Rechav K, Paul-Gilloteaux P, Avinoam O. In situ fiducial markers for 3D correlative cryo-fluorescence and FIB-SEM imaging. iScience. juill 2021;24(7):102714.

5. Kounatidis I, Stanifer ML, Phillips MA, Paul-Gilloteaux P, Heiligenstein X, Wang H, et al. 3D Correlative Cryo-Structured Illumination Fluorescence and Soft X-ray Microscopy Elucidates Reovirus Intracellular Release Pathway. Cell. juill 2020;182(2):515-530.e17.

6. Vyas N, Kunne S, Fish TM, Dobbie IM, Harkiolaki M, Paul-Gilloteaux P. Protocol for image registration of correlative soft X-ray tomography and super-resolution structured illumination microscopy images. STAR Protoc. juin 2021;2(2):100529.