Locally Developed Software
Good computer programs have always been vitally important to the work of the LMB.
Many of the groups here write, or contribute to scientific software, and wherever possible this work is released to the open source software community.
Image Processing Software
Members of Greg Jefferis' group have contributed the following:
Contributions to MicroManager, a microscope control package using a C++ core and an ImageJ front end for control of microscopes and peripherals.
Greg and Alex Hodge have contributed to the dc1394 camera adapater for generic firewire cameras.
CMTK, a software toolkit for computational morphometry of biomedical images, CMTK comprises a selection of command line tools and a general-purpose library for processing and I/O. Contributions to this package made by the group, include the development of a simple front end for CMTK which is released at flybrain.stanford.edu.
Neuronanatomy Analysis Suite Software written in R for analysis of neuronal branching patterns, 3D density data describing neuronal projections and deformation based morphometry (shape analysis of groups of co-registered brains). Includes I/O functions to allow import (and in some cases export) for:
- SWC, Neurolucida and Amiramesh neuronal tracing formats
- Biorad PIC, Nrrd, Amiramesh 2D/3D image data
Access to pre-release versions can be provided, please email Greg ( email@example.com) for details of the group’s git version control repository.
The main programs in producing a list of reflection intensities from diffraction images are:-
- MOSFLM (Andrew Leslie, Harry Powell): indexes the diffraction pattern and produces integrated reflection intensities. An interactive graphical interface iMosflm makes this easy for the user.
- POINTLESS (Phil Evans): determines the point group & space group symmetry from the list of intensities from Mosflm.
- SCALA (Phil Evans): scales symmetry-related intensities together to correct for differences in their measurement methods, averages them and produces a large variety of statistics indicating the data quality.
Semi-Automated Routines for Functional Image Analysis (SARFI)
Key features are image-based detection of structures of interest using the Laplace operator, determining the positions of units in a layered network, clustering algorithms to classify units with similar functional responses, and a database to store, exchange and analyse results across experiments. GUI access to a wide range of analysis functions for image stacks.
The custom image processing functions include thresholding based on the Laplace operator, filtering of 3D waves using principal component analysis (PCA), rotating functions, images/image stacks without interpolation, line scan analysis; Automated baseline detection, hierarchical clustering and bleach subtraction from fluorescence traces.
The package includes a manual describing the control panels and a help file that describes all functions in detail.
The SUPERFAMILY annotation is based on a collection of hidden Markov models, which represent structural protein domains at the SCOP superfamily level. A superfamily groups together domains which have an evolutionary relationship. The annotation is produced by scanning protein sequences from completely sequenced genomes against the hidden Markov models.For each protein you can:
- Submit sequences for SCOP classification
- View domain organisation, sequence alignments and protein sequence details
For each genome you can:
- Examine superfamily assignments, phylogenetic trees, domain organisation lists and networks
- Check for over- and under-represented superfamilies within a genome
For each superfamily you can:
- Inspect SCOP classification, functional annotation, Gene Ontology annotation, InterPro abstract and genome assignments
- Explore taxonomic distribution of a superfamily across the tree of life
All annotation, models and the database dump are freely available for download to everyone.