In recent years, we've focused on the OME analysis system and developing robust general image analysis methodology, culminating in our pattern recognition tool called WND-CHRM. We have validated this pattern-recognition approach to biological image analysis using diverse imaging modalities ranging from fluorescence microscopy to X-rays of human knees. We have also validated a range of applications from scoring image-based assays to diagnosis of disease to prediction of future disease risk. The specific applications of this approach are covered in reports AG000674-10 and AG000685-07. A major effort recently has been to rewrite the WND-CHARM code-base to make it more modular, better organized, easier to use, and accessible with the Python scripting language. A recent release of WND-CHARM 1.50 is available from our code repository (https://code.google.com/p/wnd-charm/), with significant speed improvements as well as several bug fixes. Most recently, a significant effort was made to integrate WND-CHARM with OMERO, resulting in a developer preview release of the integrated project in August 2014. Additionally, the Bisque development team at UC-Santa Barbara in BS Manjunath's group has been able to use our revamped code for image feature calculation in their own open-source software project. Efforts are to ongoing to finish reorganizing the WND-CHARM codebase. Whole-image analysis has proven very useful, but it is not always possible to compare whole images to each other. Examples of relatively homogenous images are those of cultured cells, or tissues like muscle, liver, and certain types of tumors. Our work on human knee X-Rays (see AG000685-07) was the first application where a certain degree of pre-processing was necessary to align images of different subjects to compare them to each other. In this case, we simply found the center of the knee joint in each image and extracted a fixed radius around this center for all patients. A much more complicated alignment problem exists in images with complex anatomy. Possibly the most extreme example of this are stained sections of brain tissue. A solution to the alignment problem would allow the use of generalized pattern recognition to address morphological differences in an anatomical context. Spatially-resolved pattern analysis places an extreme burden on the performance of our software. Instead of an entire image being considered at once, or split into a small number of tiles on a grid, to achieve spatial resolution, each image must be sampled thousands or millions of times. In order to make this type of application practical, the computational strategy used in the software must be reconsidered. Previously, all 3,000 low-level image features were calculated for each image sample, even when most of them were later found to be irrelevant to the classification problem because they lacked discrimination power. The major change in strategy to enable spatially-resolved pattern recognition is to eliminate unnecessary calculations. This requires an on-demand computing strategy for image features, which is a major architectural goal for the wndchrm software. Our current release makes use of this strategy, exposing a very simple to use API for specifying the specific features to be computed. We have have also made the majority of the underlying C++ code accessible from the Python scripting language to make it easier to customize how WND-CHARM is used in new applications. It is now possible to compute on-demand features using the Python interface and perform further processing using mathematical and scientific computing libraries available for Python (numpy, scipy). The Python-related software is publicly available on our public code repository (https://github.com/wnd-charm/wnd-charm). In 2012, in collaboration with Jason Swedlow (University of Dundee, Scotland), a large international project sponsored by the Wellcome Trust was initiated to develop specific applications of the OME/OMERO system. Our group's contribution to this project involves providing interfaces between OMERO and WND-CHARM to enable image comparisons in large, diverse image repositories. The eventual goal is to use pattern recognition to annotate new images added to these collections automatically, based on previously annotated images and a large set of independent classifiers that opeerate autonomously in the background. The primary design goal of a system like OME/OMERO is to provide scientists with easy ways of organizing and annotating their image collections. The organizational structure of the images and their grouping by their annotations can also serve as the primary inputs for training pattern-recognition classifiers. Because classifiers require little or no additional input from the user, the natural convergence of these two technologies represent a powerful new mode for maximizing the utility of large scale scientific and medical image databases. Currently we have a functioning prototype that interacts with OMERO to read image data and annotations;use these for training a classifier;and return annotations derived from classification back to OMERO. Substantial work remains to make this integrated system practical. The current developer-preview release lacks flexibility on the OMERO side to keep track of multiple, potentially conflicting classifications for images, as well as maintain a flexible store of image feature sets. Additionally, both the OMERO and the Python-WND-CHARM software packages need better support for sub-image regions (ROIs) and systematic image tiling schemes. Despite these limitations, the released software is capable of training a classifier and using it to classify previously unseen images.
| Du, Wei; Cheung, Huey; Goldberg, Ilya et al. (2015) A Longitudinal Support Vector Regression for Prediction of ALS Score. IEEE Int Conf Bioinform Biomed Workshops 2015:1586-1590 |
| Masuzzo, Paola; Martens, Lennart; 2014 Cell Migration Workshop Participants et al. (2015) An open data ecosystem for cell migration research. Trends Cell Biol 25:55-8 |
| Smith, Barry; Arabandi, Sivaram; Brochhausen, Mathias et al. (2015) Biomedical imaging ontologies: A survey and proposal for future work. J Pathol Inform 6:37 |
| Eliceiri, Kevin W; Berthold, Michael R; Goldberg, Ilya G et al. (2012) Biological imaging software tools. Nat Methods 9:697-710 |
| Orlov, Nikita V; Eckley, D Mark; Shamir, Lior et al. (2012) Improving class separability using extended pixel planes: a comparative study. Mach Vis Appl 23:1047-1058 |
