İmren Dinç

FocusALL: Focal Stacking of Microscopic Images Using Modified Harris Corner Response Measure

Automated image analysis of microscopic images such as protein crystallization images and cellular images is one of the important research areas. If objects in a scene appear at different depths with respect to the cameras focal point, objects outside the depth of field usually appear blurred. Therefore, scientists capture a collection of images with different depths of field. Focal stacking is a technique of creating a single focused image from a stack of images collected with different depths of field. In this paper, we introduce a novel focal stacking technique, FocusALL, which is based on our modified Harris Corner Response Measure. We also propose enhanced FocusALL for application on images collected under high resolution and varying illumination. FocusALL resolves problems related to the assumption that focus regions have high contrast and high intensity. Especially, FocusALL generates sharper boundaries around protein crystal regions and good in focus images for high resolution images in reasonable time. FocusALL outperforms other methods on protein crystallization images and performs comparably well on other datasets such as retinal epithelial images and simulated datasets.

Optimizing Associative Experimental Design for Protein Crystallization Screening

The goal of protein crystallization screening is the determination of the main factors of importance to crystallizing the protein under investigation. One of the major issues about determining these factors is that screening is often expanded to many hundreds or thousands of conditions to maximize combinatorial chemical space coverage for maximizing the chances of a successful (crystalline) outcome. In this paper, we propose an experimental design method called “Associative Experimental Design (AED)” and an optimization method includes eliminating prohibited combinations and prioritizing reagents based on AED analysis of results from protein crystallization experiments. AED generates candidate cocktails based on these initial screening results. These results are analyzed to determine those screening factors in chemical space that are most likely to lead to higher scoring outcomes, crystals. We have tested AED on three proteins derived from the hyperthermophile Thermococcus thioreducens, and we applied an optimization method to these proteins. Our AED method generated novel cocktails (count provided in parentheses) leading to crystals for three proteins as follows: Nucleoside diphosphate kinase (4), HAD superfamily hydrolase (2), Nucleoside kinase (1). After getting promising results, we have tested our optimization method on four different proteins. The AED method with optimization yielded 4, 3, and 20 crystalline conditions for holo Human Transferrin, archaeal exosome protein, and Nucleoside diphosphate kinase, respectively.

Evaluation of semi-supervised learning for classification of protein crystallization imagery

In this paper, we investigate the performance of two wrapper methods for semi-supervised learning algorithms for classification of protein crystallization images with limited labeled images. Firstly, we evaluate the performance of semi-supervised approach using self-training with naïve Bayesian (NB) and sequential minimum optimization (SMO) as the base classifiers. The confidence values returned by these classifiers are used to select high confident predictions to be used for self-training. Secondly, we analyze the performance of Yet Another Two Stage Idea (YATSI) semi-supervised learning using NB, SMO, multilayer perceptron (MLP), J48 and random forest (RF) classifiers. These results are compared with the basic supervised learning using the same training sets. We perform our experiments on a dataset consisting of 2250 protein crystallization images for different proportions of training and test data. Our results indicate that NB and SMO using both self-training and YATSI semi-supervised approaches improve accuracies with respect to supervised learning. On the other hand, MLP, J48 and RF perform better using basic supervised learning. Overall, random forest classifier yields the best accuracy with supervised learning for our dataset.

Protein Crystallization Screening Using Associative Experimental Design

Protein crystallization remains a highly empirical process. The purpose of protein crystallization screening is the determination of the main factors of importance leading to protein crystallization. One of the major problems about determining these factors is that screening is often expanded to many hundreds or thousands of conditions to maximize combinatorial chemical space coverage for a successful (crystalline) outcome. In this paper, we propose a new experimental design method called “Associative Experimental Design (AED)” that provides a list of screening factors that are likely to lead to higher scoring outcomes or crystals by analyzing preliminary experimental results. We have tested AED on Nucleoside diphosphate kinase, HAD superfamily hydrolase, and nucleoside kinase proteins derived from the hyperthermophile Thermococcus thioreducens [1]. After obtaining the candidate novel conditions, we have confirmed that AED method yielded high scoring crystals after experimenting in a wet lab.

Automatic classification of protein crystal images

Abstract This work introduces our method for automatic classification of crystallization trial images according to the types of protein crystals present in the images. The images are classified into four categories: needles, small crystals, large crystals, and other crystals. Because protein crystals are characterized by some geometric shapes, we focus on extracting geometric features from the images. Our image feature extraction includes extraction of blob features from multiple binary images, extraction of edge related features from Canny edge image, and extraction of line features using Hough line transform. For the decision model, we propose applying random forest classifier. We performed our experiments on 212 expert labeled images with different classifiers and tested our results using 10-fold cross validation. The proposed classification technique produces a reasonable performance for protein crystallization image classification. The overall accuracy using random forest is 78%.

Super-Thresholding: Supervised Thresholding of Protein Crystal Images

In general, a single thresholding technique is developed or enhanced to separate foreground objects from background for a domain of images. This idea may not generate satisfactory results for all images in a dataset, since different images may require different types of thresholding methods for proper binarization or segmentation. To overcome this limitation, in this study, we propose a novel approach called “super-thresholding” that utilizes a supervised classifier to decide an appropriate thresholding method for a specific image. This method provides a generic framework that allows selection of the best thresholding method among different thresholding techniques that are beneficial for the problem domain. A classifier model is built using features extracted priori from the original image only or posteriori by analyzing the outputs of thresholding methods and the original image. This model is applied to identify the thresholding method for new images of the domain. We performed our method on protein crystallization images, and then we compared our results with six thresholding techniques. Numerical results are provided using four different correctness measurements. Super-thresholding outperforms the best single thresholding method around 10 percent, and it gives the best performance for protein crystallization dataset in our experiments.

Feature analysis for classification of trace fluorescent labeled protein crystallization images

BackgroundLarge number of features are extracted from protein crystallization trial images to improve the accuracy of classifiers for predicting the presence of crystals or phases of the crystallization process. The excessive number of features and computationally intensive image processing methods to extract these features make utilization of automated classification tools on stand-alone computing systems inconvenient due to the required time to complete the classification tasks. Combinations of image feature sets, feature reduction and classification techniques for crystallization images benefiting from trace fluorescence labeling are investigated.ResultsFeatures are categorized into intensity, graph, histogram, texture, shape adaptive, and region features (using binarized images generated by Otsu’s, green percentile, and morphological thresholding). The effects of normalization, feature reduction with principle components analysis (PCA), and feature selection using random forest classifier are also analyzed. The time required to extract feature categories is computed and an estimated time of extraction is provided for feature category combinations. We have conducted around 8624 experiments (different combinations of feature categories, binarization methods, feature reduction/selection, normalization, and crystal categories). The best experimental results are obtained using combinations of intensity features, region features using Otsu’s thresholding, region features using green percentile G90 thresholding, region features using green percentile G99 thresholding, graph features, and histogram features. Using this feature set combination, 96% accuracy (without misclassifying crystals as non-crystals) was achieved for the first level of classification to determine presence of crystals. Since missing a crystal is not desired, our algorithm is adjusted to achieve a high sensitivity rate. In the second level classification, 74.2% accuracy for (5-class) crystal sub-category classification. Best classification rates were achieved using random forest classifier.ContributionsThe feature extraction and classification could be completed in about 2 s per image on a stand-alone computing system, which is suitable for real time analysis. These results enable research groups to select features according to their hardware setups for real-time analysis.

Evaluation of Normalization and PCA on the Performance of Classifiers for Protein Crystallization Images

In this paper, we investigate the performance of classification of protein crystallization images captured during protein crystal growth process. We group protein crystallization images into 3 categories: noncrystals, likely leads (conditions that may yield formation of crystals) and crystals. In this research, we only consider the subcategories of noncrystal and likely leads protein crystallization images separately. We use 5 different classifiers to solve this problem and we applied some data preprocessing methods such as principal component analysis (PCA), min-max (MM) normalization and z-score (ZS) normalization methods to our datasets in order to evaluate their effects on classifiers for the noncrystal and likely leads datasets. We performed our experiments on 1606 noncrystal and 245 likely leads images independently. We had satisfactory results for both datasets. We reached 96.8% accuracy for noncrystal dataset and 94.8% accuracy for likely leads dataset. Our target is to investigate the best classifiers with optimal preprocessing techniques on both noncrystal and likely leads datasets.

DT-Binarize: A decision tree based binarization for protein crystal images

In image thresholding problems, there are some cases that single thresholding technique may not generate good binary images for all samples. Using multiple methods may help to overcome this limitation, but this idea brings another problem. It is not a trivial task to select proper thresholding method for each image in the dataset. In this study, we propose a generic framework for image thresholding that utilizes a tree based structure to determine the best thresholding approach for a particular case. We call our method “DT-Binarize,” and apply our method to the protein crystallization image dataset. In our experiments, we compare the results with the reference binary images that are manually generated by our research group. In order to provide more reliable and objective comparison, numerical results are presented as well as the visual results. Experimental results indicate that the correctness of DT-Binarize outperforms other methods by 10% on the average.

Autofocusing for microscopic images using Harris Corner Response Measure

One of the difficulties for proper imaging in microscopic image analysis is defocusing. Microscopic images such as cellular images, protein images, etc. need properly focused image for image analysis. A small difference in focal depth affects the details of an object significantly. In this paper, we introduce a novel auto-focusing approach based on Harris Corner Response Measure (HCRM) and compare the performance with some existing auto-focusing methods. We perform our experiments on protein images as well as a simulated image stack to evaluate the performance of our method. Our results show that our HCRMbased technique outperforms other techniques.