diff --git a/README.md b/README.md index f3650e44b5b42129a3fb3e3ddba1f25eb77b4760..54080be3b8e92dfec2d33e3b8994b86193361127 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,10 @@ -# eigenpsf-extractor +# EigenPSFExtractor -EigenPSFExtactor allows you to finely characterization of your optical system from images of isolated sources (fluorescent microbeads, guide stars, ...) +EigenPSFExtactor allows you to finely characterize your optical system from images of isolated sources (fluorescent microbeads, guide stars, ...) It based on a set of accuracte routines to detect, register, process and average the diffracted sources images. The plugin is rock solid for 2D images. -Beware: the treatment of 3D images is slow, because this version is based on Java only. Use it at your own risks. +**Beware:** the treatment of 3D images is slow, because this version is based on Java only. Use it at your own risks. ## Citation @@ -23,23 +23,23 @@ Once the site has been added, updating Fiji should cause it to download and inst ## How it works? 1. Open Fiji -2. Open Plugins -> Eigen_PSF -> Eigen_PSF +2. Open *Plugins -> Eigen_PSF -> Eigen_PSF*  -3. Drag and drop the images you want to open in the left pane. +3. **Drag and drop the images** you want to open in the left pane.  -4. You can display the selected images by clicking on the eye (show) in the left pane. +4. **Display the selected images** by clicking on the eye (show) in the left pane.  5. Click on the parameters button and set the parameters. In particular, pay attention to : - - Set 2D/3D option - - Set the width of a PSF. You can also do it by drawing a square around a PSF and by clicking on get_ROI - - Set the number of EigenPSFs (this can be done afterwards) + - **Set 2D/3D option**. + - **Set the PSF width**. You can also do it by drawing a square around a PSF and by clicking on get_ROI. + - **Set the number of EigenPSFs** (this can be done afterwards as well).  @@ -63,10 +63,26 @@ Once the site has been added, updating Fiji should cause it to download and inst ## Future releases +The current code is based purely on Java. Unfortunately, some operations (convolutions with FFTs) are resource intensive. We plan to: +1. Develop a Pytorch package. +2. Bind the current Java/Fiji interface with this code. +3. Develop a Napari plugin for a better Pytorch integration. + ## Contributing If you want to contribute to this project, do not hesitate to contact the core developing team. -## License +valentin.debarnot@gmail.com +emmanuel.soubies@irit.fr +daniel.sage@epfl.ch +pierre.weiss@cnrs.fr + +## References + +This work heavily relies on the following references. + +V. Debarnot, P. Escande, T. Mangeat and P. Weiss, "Learning Low-Dimensional Models of Microscopes," in IEEE Transactions on Computational Imaging, vol. 7, pp. 178-190, 2021, doi: 10.1109/TCI.2020.3048295. +Debarnot, V., & Weiss, P. (2023). Blind inverse problems with isolated spikes. Information and Inference: A Journal of the IMA, 12(1), 26-71. +Bigot, J., Escande, P., & Weiss, P. (2019). Estimation of linear operators from scattered impulse responses. Applied and Computational Harmonic Analysis, 47(3), 730-758.