From 0c83bfab395c96b7d6aa3155f3ce9017be84514c Mon Sep 17 00:00:00 2001
From: Moritz Wachsmuth-Melm <3951290+MoritzWM@users.noreply.github.com>
Date: Mon, 17 Aug 2020 10:08:35 +0200
Subject: [PATCH] Initial commit of README

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+# Post-correlation cryo-CLEM toolbox
+
+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 [our paper](https://doi.org/10.1101/2020.02.27.966739).
+
+## FIJI plugin
+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 StitchTileScan 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 ROIExtractor 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 StitchTileScan command) and and output directory.
+The stitched image will be opened and overlaid with the positions of the individual tiles.
+Whenever you click into a tile, 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.
+
+## 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.