Utilities

This section regroups the programs maintained by BioCAT and useful for X-ray images users.

Chiplot Analyze

Chiplot-analyze is a utility program designed to take as input 1D traces of the integrated intensity along rectangular boxed shaped regions aligned along either the equator, the meridian, or along a layer line using the program FIT2D and saved as “chiplot” files. Chiplot files are an ASCIII format and are easily readable in various ways. What chiplot-analyze does is take one of these traces and splits into two halves containing symmetrical diffraction patterns from the left or right (if trace is from the equator or a layer line) or top and bottom (if trace is along the meridian). You can then subtract a continuous background for the trace using a convex hull algorithm and save the background subtracted trace in a new file. The background subtracted trace can then be input into various peak fitting programs for further analysis. In the Irving lab this is usually the Fityk program which allows defining custom peak functions. The final thing chiplot-analyze can do is to calculate the centroid and integrated of user defined diffraction peaks and save the results to a file.

• Github code

• Windows, Mac, Deb package installers: Chiplot Analyze on SourceForge

• Pip install: pip install chiplot-analyze

HDF5 to TIFF Converter

Note

Starting in MuscleX 1.22.0, H5 files can directly be read, processed, and analyzed by MuscleX modules.

Simple program to convert HDF5 files to TIFF images.

• Available inside the MuscleX code: Github code

• Pip version: pip install hdf5-to-tiff

• Windows installer and AppImage: HDF5 to TIFF Converter on SourceForge

Click here to learn more about the program and how it works.

TIFF Compressor-Decompressor

Simple program to compress or decompress TIFF images. Uses tiff_lzw format (lossless).

• Available inside the MuscleX code: Github code

• Pip version: pip install tif-compressor

• Windows installer and AppImage: TIFF Compressor-Decompressor on SourceForge

Click here to learn more about the program and how it works.

Strong image creator

Simple program to create strong images from a set of TIFF images, or from h5 files containing single images.

• Available inside the MuscleX code: Github code

• Pip version: pip install strong-image-creation

A more advanced version of this program is available under the name “AISE”.