Manuals

Fiducialisation and grid preparation - this is a quick guide on how to prepare grids prior to tissue culture as well as the current standard at B24 for fiducialisation.

Plunge freezing - step-by-step protocol for vitrification of biological samples at B24 on TEM grids.

Cryo-SIM

• User manual (new version of cockpit)
• concise protocol (old version of cockpit)
• expanded user manual: (old version of cockpit) 
• JoVE protocol and video outlining steps for acquiring super-resolution fluorescence images using the cryo-SIM.

Batch proecssing of raw structured illumination (SIM) data to pseudo wide-field using this custom-written Fiji macro. Please note that the SIMCheck plugin needs to be installed in Fiji before this macro will work.

Batch intensity projection of processes structured illumination (SIM) data using this custom-written Fiji macro.

TXRM - step-by-step protocol for mosaic and tilt series acquisition using B24's transmission X-ray microscope (TXRM).

Tomogram reconstruction 

• Start here: Quick start guide for tomogram reconstruction at B24
• Online tutorial on how to use etomo in IMOD for tomogram reconstruction
• Resource files for practicing tomogram reconstruction with IMOD
• A PowerPoint presentation from a B24 workshop on how to use IMOD for tilt series reconstruction into a tomogram. 

Project data organisation - a concise guide on directory structure during data sorting.

Correlation

• Start here: Quick start guide for correlation of B24 data
• a STAR protocols paper on using eC-CLEM for 2D and 3D correlation of fluorescence and X-ray images
•  video tutorial showing correlation usig eC-CLEM and chromatic shift correction using Chromagnon

Image analysis - a concise guide on how to write Macros for automated image analysis with Fiji (ImageJ).

Segmentation​​​

• Start here: Quick start guide for SXT segmentation
• Contour Instruction guide
• Quick guide to using Fiji segmentation editor