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NanoJ-eSRRF

Features of eSRRF

Some of the new features available in eSRRF are as follows:

• improved fidelity of reconstructions
• adaptive reconstruction schemes allowing to explore the compromises between fidelity and resolution. This is enabled by an integration of our SQUIRREL approach (SQUIRREL paper).
• estimation of the maximum number of frames to use for eSRRF analysis from a dataset, based on SSIM (or optical flow magnitude) calculation
• rolling analysis
• integrated drift correction
• better memory management
• full OpenCL integration
• direct saving to disk for large dataset analysis
• eSRRF 3D reconstruction!

Installation guide

The latest stable version of eSRRF can be directrly obtained from our Fiji update site:

https://sites.imagej.net/NanoJ-LiveSRRF/

Information about update sites can be found here.

Video guide: Installation

There have been some issues reported with OpenCl and running NanoJ-Squirrel and NanoJ-eSRRF on Windows10/11. You can find an instruction with the temporal fix in the below.

✨ ✨ Update November 2023 ✨ ✨:

eSRRF is now also available in Python 🐍! You'll find the code and notebooks here: 👉 https://github.com/HenriquesLab/NanoPyx

✨ ✨ ✨ ✨ ✨ ✨ ✨ ✨ ✨ ✨ ✨ ✨

Test datasets

We have published test datasets including eSRRF parameter suggestions on Zenodo. Download and get started right away!

Video guide: Getting started

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How to use eSRRF

Please use the various links on the side bar to the right to learn to use the different functionalities of eSRRF. You will find information about what the parameters are and how to use them.

Contributing and testing eSRRF

Whether you like the plugin, use it or hate it, if you have some comments, suggestions or feedback, please feel free to add entries to our issue page, and we'll try out best to address these!

NanoJ-eSRRF OpenCl issues

There have been some issues reported when using NanoJ-eSRRF on Windows 10/11 machines and regarding general OpenCl compatibility. We propose the following temporary fix until we release an updated version:

• Close Fiji

• Install the OpenCL™ and OpenGL® Compatibility Pack (https://apps.microsoft.com/store/detail/opencl%E2%84%A2-and-opengl%C2%AE-compatibility-pack/9NQPSL29BFFF?hl=en-us&gl=us&activetab=pivot%3Aoverviewtab)

• Either update eSRRF via the update site: https://sites.imagej.net/NanoJ-LiveSRRF or manually exchange the libraries as described in the following steps:

  • Go to the folder /.../Fiji.app/jars and remove these .jar files:
  1. jogl-all-2.4.0-rc-20211011.jar
  2. jocl-all-2.4.0-rc-20211011.jar
  3. joal-all-2.4.0-rc-20211011.jar
  4. gluegen-rt-2.4.0-rc-20210111.jar
  • Go to:  https://jogamp.org/deployment/archive/rc/v2.5.0-rc-20230523/jar/ and download the following files: jogl-all.jar, jocl.jar, joal.jar, gluegen.jar
  • Place these four files in the folder /.../Fiji.app/jars
  • Go to the folder /.../Fiji.app/jars/win64 and remove these .jar files: 
  1. gluegen-rt-2.4.0-rc-20210111-natives-windows-amd64.jar
  2. joal-2.4.0-rc-20210111-natives-windows-amd64.jar
  3. jocl-2.4.0-rc-20210111-natives-windows-amd64.jar
  • Go to:  https://jogamp.org/deployment/archive/rc/v2.5.0-rc-20230523/jar/ and download the following files: gluegen-rt-natives-windows-amd64.jar, jocl-natives-windows-amd64.jar, joal-natives-windows-amd64.jar
  • Place these three files in the folder /.../Fiji.app/jars/win64
  • Restart Fiji

Now all NanoJ plugins should work.

If you run eSRRF make sure to have the following settings: Advanced settings > Processing device > Default device