Manuals for B24 instruments, techniques and workflow:
- 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 - concise protocol or expanded user manual outlining steps for acquiring super-resolution fluorescence images using the cryo-SIM.
- TXRM - step-by-step protocol for mosaic and tilt series acquisition using B24's transmission X-ray microscope (TXRM).
- Reconstruction - a PowerPoint presentation from a B24 workshop on how to use IMOD for tilt series reconstruction into a tomogram.
- Correlation - a guide on using eC-CLEM for 2D and 3D correlation of fluorescence and X-ray images.
- Image analysis - a concise guide on how to write Macros for automated image analysis with Fiji (ImageJ).
- StitchM: a Python 3 package with a command line interface. StitchM creates a flat mosaic image from the cryoSIM brighfield data. Regions of interest can be added with the OME-TIFF standard, viewable with Bioformats in ImageJ/Fiji.
- txrm2tiff: a Python 3 package with a command line interface. txrm2tiff converts the raw data from the SXM into tiff files, a widely-supported lossless format. This is has been developed for B24 as part of our automatic processing pipeline.
- GridSNAP: currently undergoing commissioning, this software offers a web-based GUI for semi-automatically alignment 2D brightfield images from the cryoSIM and SXT. This enables a coordinate transform between microscopes, which ensures that the regions of interest from the cryoSIM can be quickly identified and imaged on the SXM. GridSNAP also ouputs transform data that can later be used as a starting point when correlating the 3D data sets.
- omexml-dls: a Python 2/3 module for creating and interacting with OME xml metadata. This was created for lightweight access to OME metadata by B24's software.
- SuRVoS: Super Region Volume Segmentation.
- IMOD: a set of image processing, modeling and display programs used for tomographic reconstruction. IMOD's batchruntomo is used by our automatic processing pipeline and we recommend IMOD's etomo for manual reconstruction.
- eC-CLEM: a plugin of Icy for multidimensional image alignment in 2D or 3D.
- Fiji (Fiji is just ImageJ): an image processing package, ImageJ, bundled with commonly used plugins. Our commonly used plugins include:
- SIMCheck: a suite for super-resolution structured illumination microscopy data quality control.
- Bioformats: for reading and writing life sciences image file formats (including OME metadata).