Software

In-house software and scripts

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: this software offers semi-automatic alignment 2D of brightfield images from the cryoSIM and SXT to easily transfer regions of interest (ROIs) from the cryoSIM can to the the SXM.

XMBatch: user-friendly software for queueing up batches of scans on the TXM.

Fluorescence Merging Macro: for merging and flattening SIM fluorescence images in Fiji. To download, right click this link and select "Save as...".

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.

SuRVoS: Super Region Volume Segmentation.

Recommendations

Chromagnon: Open source software for chromatic shift correction of fluorescence images

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).

Reference Library

B24 has a continually updated Endnote Library list with relevant references for TXM, SIM and correlation. We are happy to share this with you; please contact any of the B24 team, tell us your email address and we will send you a link to the library.