This repository contains utilities to help with the on-lamella post-correlation cryo-CLEM workflow developed in the Chlanda Lab at Heidelberg University. For more information, see the following publications:
Post-correlation on-lamella cryo-CLEM reveals the membrane architecture of lamellar bodies
To download the latest version, please see the Releases page
To install the FIJI plugin, copy the file 'cryoCLEM-x.x.x.jar' to the FIJI plugin folder (FIJI/plugins). Make sure to delete any older versions of the plugin. After sucessful installation, the plugin can be be found in the FIJI submenu "Plugins - CryoCLEM".
The Matlab script 'Align_cLM_Stack.m' does not need to be installed. It can be directly loaded and run in Matlab.
The FIJI plugin helps with handling the Z-stack tile scan acquired on the Leica cryo-CLEM wide-field microscope. The files are usually large (>100 GB) and therefore cannot be opened with FIJI or other image processing software.
The "Stitch Tile Scan" command runs a maximum projection on a tilescan and stitches it to one image. This is useful for targeted cryo-FIB milling, as the image (exported as a PNG file) can be overlaid with an EM map of the grid using MAPS (ThermoFisher).
The "Get ZStacks from stitch" command allows you to easily extract single Z-stacks from the previously stitched map. You just need the original tile scan, the ROIset file and the stitched image (both are created by the "Stitch Tile Scan" command) and an output directory. The stitched image will be opened and overlaid with the positions of the individual tiles. Whenever you click the number of a tile (slection tool need to be enabled), the corresponding Z-stack will be extracted from the original tile scan and written into the output directory as a .tif. These are subsequently used for deconvolution and correlation with the matlab script.
The matlab script performs 3D rigid registration of two Z-stacks, one pre milling (pre-LM map) and one post EM acquisition (post-LM map), calculating a transformation matrix which is applied to the post-LM map.