Faster shading by equal angle interpolation of vectors

In this paper, we show how spherical linear interpolation can be used to produce shading with a quality at least similar to Phong shading at a computational effort in the inner loop that is close to that of the Gouraud method. We show how to use the Chebyshev's recurrence relation in order to compute the shading very efficiently. Furthermore, it can also be used to interpolate vectors in such a way that normalization is not necessary, which will make the interpolation very fast. The somewhat larger setup effort required by this approach can be handled through table look up techniques.

Abnormal expression pattern of cyclin E in tumour cells

The expression pattern of cyclin E during the cell cycle was studied in normal and tumour cells in culture and in tumour biopsies. This pattern was found to be abnormal in tumour cells. A triple immunostaining protocol, digital microscopy and image analysis were used to find the position of the individual cells in the cell cycle and to measure the nuclear cyclin E levels. In normal cells, the number of cyclin E-positive cells decreased rapidly when the cells entered the S-phase. In the tumour cell lines, cyclin E was not downregulated in early S-phase, as in normal cells. Instead the number of cyclin E-positive cells remained high throughout S-phase, and the cyclin E staining intensity per cell often increased during S-phase. In about half of the analysed tumour cell lines, many cells stained positive for cyclin E even in the G(2)-phase. This abnormal expression over the cell cycle of cyclin E was also found in tumour biopsies from cervical, breast and prostatic carcinomas, even though it varied greatly between individual tumours. In some tumours, the expression pattern of cyclin E was similar to that of normal cells in culture, whereas in others high cyclin E levels could be seen in S-phase cells, as in the transformed cell lines. A high percentage of cells expressing cyclin E during S- or G(2)-phase was found to be related to poor outcome (p < 0.025) in a small group of cervical carcinoma patients (n = 12).

A feature set for cytometry on digitized microscopic images

Feature extraction is a crucial step in most cytometry studies. In this paper a systematic approach to feature extraction is presented. The feature sets that have been developed and used for quantitative cytology at the Laboratory for Biomedical Image Analysis of the GSF as well as at the Center for Image Analysis in Uppsala over the last 25 years are described and illustrated. The feature sets described are divided into morphometric, densitometric, textural and structural features. The latter group is used to describe the eu- and hetero-chromatin in a way complementing the textural methods. The main goal of the paper is to bring attention to the need of a common and well defined description of features used in cyto- and histometrical studies. The application of the sets of features is shown in an overview of projects from different fields. Finally some rules of thumb for the design of studies in this field are proposed. Colour figures can be viewed on http://www.esacp.org/acp/2003/25-1/rodenacker.htm.

Automatic registration and error detection of multiple slices using landmarks

OBJECTIVES

When analysing the 3D structure of tissue, serial sectioning and staining of the resulting slices is sometimes the preferred option. This leads to severe registration problems. In this paper, a method for automatic registration and error detection of slices using landmark needles has been developed. A cost function takes some parameters from the current state of the problem to be solved as input and gives a quality of the current solution as output. The cost function used in this paper, is based on a model of the slices and the landmark needles. The method has been used to register slices of prostates in order to create 3D computer models. Manual registration of the same prostates has been undertaken and compared with the results from the algorithm.

METHODS

Prostates from sixteen men who underwent radical prostatectomy were formalin fixed with landmark needles, sliced and the slices were computer reconstructed. The cost function takes rotation and translation for each prostate slice, as well as slope and offset for each landmark needle as input. The current quality of fit of the model, using the input parameters given, is returned. The function takes the built-in instability of the model into account. The method uses a standard algorithm to optimize the prostate slice positions. To verify the result, s standard method in statistics was used.

RESULTS

The methods were evaluated for 16 prostates. When testing blindly, a physician could not determine whether the registration shown to him were created by the automated method described in this paper, or manually by an expert, except in one out of 16 cases. Visual inspection and analysis of the outlier confirmed that the input data had been deformed. The automatic detection of erroneous slices marked a few slices, including the outlier, as suspicious.

CONCLUSIONS

The model based registration performs better than traditional simple slice-wise registration. In the case of prostate slice registration, other aspects, such as the physical slicing method used, may be more important to the final result than the selection of registration method to use.

Sequential immunofluorescence staining and image analysis for detection of large numbers of antigens in individual cell nuclei

BACKGROUND

Visualization of more than one antigen by multicolor immunostaining is often desirable or even necessary to explore spatial and temporal relationships of functional significance. Previously presented staining protocols have been limited to the visualization of three or four antigens.

METHODS

Immunofluorescence staining was performed both on slices of formalin-fixed tissue and on cells in culture. Images of the stained material were recorded using digital imaging fluorescence microscopy. The primary and secondary antibodies, as well as the fluorophores, were thereafter removed using a combination of denaturation and elution techniques. After removal of the fluorescence stain, a new immunofluorescence staining was performed, visualizing a new set of antigens. The procedure was repeated up to three times. A method for image registration combined with segmentation, extraction of data, and cell classification was developed for efficient and objective analysis of the image data.

RESULTS

The results show that immunofluorescence stains in many cases can be repeatedly removed without major effects on the antigenicity of the sample.

CONCLUSIONS

The concentration of at least six different antigens in each cell can thus be measured semiquantitatively using sequential immunofluorescence staining and the described image analysis techniques. The number of antigens that can be visualized in a single sample is considerably increased by the presented protocol.

Algorithms for cytoplasm segmentation of fluorescence labelled cells

Automatic cell segmentation has various applications in cytometry, and while the nucleus is often very distinct and easy to identify, the cytoplasm provides a lot more challenge. A new combination of image analysis algorithms for segmentation of cells imaged by fluorescence microscopy is presented. The algorithm consists of an image pre-processing step, a general segmentation and merging step followed by a segmentation quality measurement. The quality measurement consists of a statistical analysis of a number of shape descriptive features. Objects that have features that differ to that of correctly segmented single cells can be further processed by a splitting step. By statistical analysis we therefore get a feedback system for separation of clustered cells. After the segmentation is completed, the quality of the final segmentation is evaluated. By training the algorithm on a representative set of training images, the algorithm is made fully automatic for subsequent images created under similar conditions. Automatic cytoplasm segmentation was tested on CHO-cells stained with calcein. The fully automatic method showed between 89% and 97% correct segmentation as compared to manual segmentation.

The amino-terminal part of PRELP binds to heparin and heparan sulfate

PRELP (proline, arginine-rich end leucine-rich repeat protein) is an extracellular matrix leucine-rich repeat protein. The amino-terminal region of PRELP differs from that of other leucine-rich repeat proteins in containing a high number of proline and arginine residues. The clustered proline and basic residues are conserved in rat, bovine, and human PRELP. Although the function of PRELP is not yet known, the clustered arginine residues suggest a heparan sulfate/heparin-binding capacity. We show here that PRELP indeed binds heparin and heparan sulfate. Truncated PRELP without the amino-terminal region does not bind heparin. The dissociation constant for the interaction of PRELP with heparin was determined by an in solution binding assay and by surface plasmon resonance analysis to be in the range of 10-30 nm. A 6-mer heparin oligosaccharide was the smallest size showing binding to PRELP. The binding increased with increasing length up to an 18-mer and depended on the degree of sulfation of heparin as well as heparan sulfate. Sulfate groups at all positions were shown to be of importance for the binding. Fibroblasts bind PRELP, and this interaction is inhibited with heparin, suggesting a function for PRELP as a linker between the matrix and cell surface proteoglycans.

A detailed analysis of cyclin A accumulation at the G(1)/S border in normal and transformed cells

The temporal relationship between cyclin A accumulation and the onset of DNA replication was analyzed in detail. Five untransformed and nine transformed asynchronously growing cell cultures were investigated using a triple immunofluorescence staining protocol combined with computerized evaluation of staining intensities in individual cells. The simultaneous staining of BrdU, cyclin A, and cyclin E made it possible to determine the cell cycle position of each cell investigated. Cells at the G(1)/S border were identified on the basis of cyclin E content and were further analyzed with respect to cyclin A and BrdU content. A method was developed to calculate objective thresholds defining the highest staining intensity found in the negative cells in the population. Using the thresholds we could distinguish cells with minute amounts of cyclin A and BrdU from truly negative cells. We show that the onset of cyclin A accumulation and the start of DNA replication occurs at the same time, or deviating by a few minutes at the most. We also show that cyclin A accumulates continuously during S. This study clearly demonstrates that nuclear cyclin A can be used as a reliable marker for the S and G(2) phases in both normal and transformed interphase cells.

Paraffin section storage and immunohistochemistry. Effects of time, temperature, fixation, and retrieval protocol with emphasis on p53 protein and MIB1 antigen

It has been observed that immunoreactivity in paraffin sections decreased during storage. In this study, stored paraffin sections from both biopsy material and cultured cells were assessed for changes in immunoreactivity, using color-based image analysis to quantitate extent and intensity of the stainings. For seven of the 11 antibodies studied, storage at 20 degrees C for 16 weeks reduced the extent of immunostaining compared with that of freshly cut sections. Furthermore, increased storage temperatures resulted in a progressive loss of immunoreactivity. After 2 weeks of storage, at both 4 degrees C and 20 degrees C, p53 protein- and MIB1-antigen expression was significantly reduced regarding extent and intensity. The extent of the immunoreactivity reduced more for p53 protein than for MIB1 antigen, but the intensity did not. Boric acid was used for antigen retrieval on sections stored for 12 weeks at 20 degrees C. For both p53 protein and MIB1 antigen, this resulted in an extent and intensity of immunostaining equal to or higher than (MIB1) that obtained in freshly cut sections, using citrate buffer. Staining of cultured cells confirmed the results from biopsy material on the influence of storage temperature. Fixation time only marginally influenced the storage-related decrease in immunoreactivity. In conclusion, storage of paraffin sections leads to a varying degree of decreased immunoreactivity for several antibodies. The degree is at least partly dependent on storage time and temperature but not fixation time. However, this may be compensated for by optimizing the antigen retrieval protocol.

Cultured human fibroblasts in agarose gel as a multi-functional control for immunohistochemistry. Standardization Of Ki67 (MIB1) assessment in routinely processed urinary bladder carcinoma tissue

Immunohistochemistry (IHC) in clinical practice is hampered by lack of standardization and by subjectivity in interpretation and quantitation. This study aimed to develop a control system for IHC in routinely fixed and histoprocessed tissues. Such a system should be easy to handle in clinical practice and should reflect variations in fixation time, section thickness, section storage conditions, and staining protocols. In addition, in image analysis quantitation of immunostained tissues, when using classifiers computed on IHC-control images, the control system should be very stable. Cultured human fibroblasts were suspended in agarose, transferred into a length of tubing and stored at 4 degrees C. Three pieces of the cellgel control were separately fixed, histoprocessed, and paraffin-embedded as external controls. One piece was prepared together with each of 18 bladder carcinoma biopsies as internal controls. Slides with sections from the biopsy and all types of cellgel controls were stored at different temperatures and then stained using three different IHC protocols. The fibroblasts were homogeneously distributed in the agarose gel. Variation in section thickness did not influence immunostaining as evaluated by the MIB1 labelling index (MIB1 LI). The external controls decreased notably in MIB1 LI with increased fixation time. This was not seen in the 18 internal controls that were each fixed with a fresh biopsy. However, section storage and immunostaining conditions influenced the MIB1 expression equally in all control types and to a similar degree to the biopsies. Furthermore, colour-based image analysis quantitation of MIB1 LI in biopsies proved stable and independent of the control type used to compute the classifier.

Modeling prostate cancer distributions

OBJECTIVES

To use computer-assisted three-dimensional (3D) reconstruction to study cancer distribution in the prostate. The distributions have been determined using data from 81 prostates surgically removed because of cancer.

METHODS

The pattern of distribution was determined by reshaping (morphing) all prostates in the same size category (small, medium, large) into the same shape and by overlayering the 3D distribution of all cancers into a "unit prostate." Also, the pattern of 3D distribution was defined for small, medium, and large volume cancers.

RESULTS

The study yielded a clear, visual "scatter diagram" representation of the statistics of prostate cancer distribution. It confirmed previous general knowledge: small cancers are mainly found in the lower one third and principally in the dorsolateral part of the gland.

CONCLUSIONS

This report is part of the investigations preliminary to establishing an optimal protocol for needle biopsy of prostate cancer.

Automatic quantification of microvessel density in urinary bladder carcinoma

Seventy-three TUR-T biopsies from bladder carcinoma were evaluated regarding microvessel density, defined as microvessel number (nMVD) and cross-section endothelial cell area (aMVD). A semi-automatic and a newly developed, automatic image analysis technique were applied in immunostainings, performed according to an optimized staining protocol. In 12 cases a comparison of biopsy material and the corresponding cystectomy specimen were tested, showing a good correlation in 11 of 12 cases (92%). The techniques proved reproducible for both nMVD and aMVD quantifications related to total tumour area. However, the automatic method was dependent on high immunostaining quality. Simultaneous, semi-automatic quantification of microvessels, stroma and epithelial fraction resulted in a decreased reproducibility. Quantification in ten images, selected in a descending order of MVD by subjective visual judgement, showed a poor observer capacity to estimate and rank MVD. Based on our results we propose quantification of MVD related to one tissue compartment. When staining quality is of high standard, automatic quantification is applicable, which facilitates quantification of multiple areas and thus, should minimize selection variability.

Biopsy protocol stability in a three-dimensional model of prostate cancer: changes in cancer yield after adjustment of biopsy positions

OBJECTIVES

Transrectal ultrasound-guided prostate biopsies are often taken according to a systematic, standardized schedule. The diagnostic stability of this system was evaluated by moving the biopsies in a three-dimensional (3D) model.

METHODS

A computerized 3D reconstruction was made from each of 75 radical prostatectomy specimens. Simulated core biopsies imitated a standardized 10-biopsy protocol, including sextant biopsies. In total, 30,000 biopsies were generated by moving the standardized biopsies 1, 2, 3, and 4 mm (parallel needle shifts) or 5 degrees, 10 degrees, 15 degrees, and 20 degrees(rotation of the needle tip) in a random direction.

RESULTS

The diagnosis of the individual biopsy changed from cancer to benign or vice versa in 4.9% to 1 5.7% after 1 to 4-mm parallel needle shifts and 2.0% to 7.5% after 5 degrees to 20 degrees rotations. The corresponding figures for the final diagnosis of the 10-biopsy set were 0.8% to 9.6% and 0.5% to 3.2%. Transition zone biopsies containing cancer changed to benign more often than the other biopsies (P <0.001). Parallel needle shifts of 2 mm changed the diagnosis more often than the 15 degrees rotation (9.4% and 5.9%, respectively, P <0.001), although conveying the same overall needle shift.

CONCLUSIONS

The cancer yield of prostate biopsies is influenced even by small changes in needle positions. The transition zone biopsies are most likely to change from cancer to benign when moved. Changing the insertion point of the needle has a higher impact on cancer yield than rotating the tip.

Three-dimensional computer reconstruction of prostate cancer from radical prostatectomy specimens: evaluation of the model by core biopsy simulation

OBJECTIVES

A technique was developed for three-dimensional (3D) modeling of prostate cancer and transrectal biopsies. To test the model, the cancer yield of a simulated 10-biopsy protocol was compared with a simulated sextant protocol and with preoperative biopsies regarding cancer detection and correlation with tumor volume.

METHODS

Transrectal ultrasound-guided core biopsies were taken from 81 men according to a standardized 10-biopsy protocol that included sextant biopsies. The patients underwent radical prostatectomy and specimens were step-sectioned and whole-mounted. Cancer and the prostate capsule were outlined on the slides and the regions transferred to a computer software program developed by our group. A 3D volume of each prostate was reconstructed from the sections. Virtual core biopsy needles imitating the positions of the real biopsies were inserted into the prostate and the cancer yield was calculated. Only the standardized positions were considered in this study (ie, additional biopsies from hypoechoic foci were not accounted for).

RESULTS

Of the cancers detected with 10 standardized virtual biopsies, 24% would have remained undetected with sextant biopsies. The cancer yield of 10 virtual biopsies correlated with the preoperative biopsies (r = 0.64) and with the tumor volume (r = 0.56). A multiple regression analysis showed that the cancer yield of a simulation of 10 biopsies correlated better with tumor volume than did a simulation of sextant biopsies (P = 0.02).

CONCLUSIONS

We conclude that computer-assisted 3D reconstruction of prostate cancer can be used as a model for evaluation and optimization of biopsy protocols.

Automatic quantification of immunohistochemically stained cell nuclei using unsupervised image analysis

A method for quantification of images of immunohistochemically stained cell nuclei by computing area proportions is presented. The image is transformed by a principal component transform. The resulting first component image is used to segment the objects from the background using dynamic thresholding of the P2/A-histogram, where P2/A is a global roundness measure. Then the image is transformed into principal component hue, defined as the angle around the first principal component. This image is used to segment positive and negative objects. The method is fully automatic and the principal component approach makes it robust with respect to illumination and focus settings. An independent test set consisting of images grabbed with different focus and illumination for each field of view was used to test the method, and the proposed method showed less variation than the intraoperator variation using supervised Maximum Likelihood classification.

Automatic quantification of immunohistochemically stained cell nuclei based on standard reference cells

A fully automatic method for quantification of images of immunohistochemically stained cell nuclei by computing area proportions, is presented. Agarose embedded cultured fibroblasts were fixed, paraffin embedded and sectioned at 4 microm. They were then stained together with 4 microm sections of the test specimen obtained from bladder cancer material. A colour based classifier is automatically computed from the control cells. The method was tested on formalin fixed paraffin embedded tissue section material, stained with monoclonal antibodies against the Ki67 antigen and cyclin A protein. Ki67 staining results in a detailed nuclear texture with pronounced nucleoli and cyclin A staining is obtained in a more homogeneously distributed pattern. However, different staining patterns did not seem to influence labelling index quantification, and the sensitivity to variations in light conditions and choice of areas within the control population was low. Thus, the technique represents a robust and reproducible quantification method. In tests measuring proportions of stained area an average standard deviation of about 1.5% for the same field was achieved when classified with classifiers created from different control samples.

Automatic quantification of microvessels using unsupervised image analysis

An automatic method for quantification of images of microvessels by computing area proportions and number of objects is presented. The objects are segmented from the background using dynamic thresholding of the average component size histogram. To be able to count the objects, fragmented objects are connected, all objects are filled, and touching objects are separated using a watershed segmentation algorithm. The method is fully automatic and robust with respect to illumination and focus settings. A test set consisting of images grabbed with different focus and illumination for each field of view, was used to test the method, and the proposed method showed less variation than the intraoperator variation using manual threshold. Further, the method showed good correlation to manual object counting (r = 0.80) on an other test set.

A new method for segmentation of colour images applied to immunohistochemically stained cell nuclei

A new method for segmenting images of immunohistochemically stained cell nuclei is presented. The aim is to distinguish between cell nuclei with a positive staining reaction and other cell nuclei, and to make it possible to quantify the reaction. First, a new supervised algorithm for creating a pixel classifier is applied to an image that is typical for the sample. The training phase of the classifier is very user friendly since only a few typical pixels for each class need to be selected. The classifier is robust in that it is non-parametric and has a built-in metric that adapts to the colour space. After the training the classifier can be applied to all images from the same staining session. Then, all pixels classified as belonging to nuclei of cells are grouped into individual nuclei through a watershed segmentation and connected component labelling algorithm. This algorithm also separates touching nuclei. Finally, the nuclei are classified according to their fraction of positive pixels.

Image analysis based grading of bladder carcinoma. Comparison of object, texture and graph based methods and their reproducibility

The possibility that computerized image analysis could increase the reproducibility of grading of bladder carcinoma as compared to conventional subjective grading made by pathologists was investigated. Object, texture and graph based analysis were carried out from Feulgen stained histological tissue sections. The object based features were extracted from gray scale images, binary images obtained by thresholding the nuclei and several other images derived through image processing operations. The textural features were based on the spatial gray-tone co-occurrence probability matrices and the graph based features were extracted from the minimum spanning trees connecting all nuclei. The large numbers of extracted features were evaluated in relation to subjective grading and to factors related to prognosis using multivariate statistical methods and multilayer backpropagation neural networks. All the methods were originally developed and tested on material from one patient and then tested for reproducibility on entirely different patient material. The results indicate reasonably good reproducibility for the best sets of features. In addition, image analysis based grading showed almost identical correlation to mitotic density and expression of p53 protein as subjective grading. It should thus be possible to use this kind of image analysis as a prognostic tool for bladder carcinoma.

The primary structure of a basic leucine-rich repeat protein, PRELP, found in connective tissues

We have determined the primary structure of a connective tissue matrix protein from the nucleotide sequence of a clone isolated from a human articular chondrocyte cDNA library. The major part of the amino acid sequence has also been determined by direct protein sequencing. The translated primary sequence corresponds to 382 amino acid residues, including a 20-residue signal peptide. The molecular mass of the mature protein is 41,646 Da. The main part of the protein consists of 10 leucine-rich repeats ranging in length from 20 to 26 residues, with asparagine at position 10 (B-type). The N-terminal part is unusual in that it is basic and rich in arginine and proline. There are four potential N-linked glycosylation sites present. In three of these sites, post-translational modifications are likely to be present since Asn was not found by direct protein sequencing. The amino- and carboxyl-terminal parts contain four and two cysteine residues, respectively, probably forming disulfide bonds by analogy with the other members of this family. The protein shows highest identity (36%) to fibromodulin and 33% to bovine lumican, two other leucine-rich repeat connective tissue proteins. Northern blot analysis showed the presence of an approximately 3.8-kilobase mRNA in different types of bovine cartilage and cultured osteoblasts, whereas RNAs isolated from bovine kidney, skin, spleen, thymus, and trabecular bone and rat calvaria were negative. Human articular chondrocyte and rat chondrosarcoma cell RNAs contained an additional mRNA of approximately 1.6 and 1.8 kilobases, respectively.

CBA--an atlas-based software tool used to facilitate the interpretation of neuroimaging data

CBA, a software tool used to improve quantification and evaluation of neuroimaging data has been developed. It uses a detailed 3-dimensional brain atlas that can be adapted to fit the brain of an individual patient represented by a series of displayed images. Anatomical information from the atlas can then be introduced into the images. If the patient has been imaged in different modalities, adaptation of the atlas to the different images will provide the transformation that brings the images into registration. CBA can thus be used as a tool for fusing multimodality information from the same patient. Furthermore, by applying the inverse atlas transformation, images from a patient can be transformed to conform to the anatomy of the atlas brain. This anatomical standardization, where the atlas brain itself serves as the anatomy standard, brings data from different individuals into a compatible form providing possibilities to perform individual-group and group-by-group comparisons between patients and normal controls.

Grading of transitional cell bladder carcinoma by image analysis of histological sections

Image analysis of histological sections was used to achieve a more objective malignancy grading of transitional cell carcinoma of the bladder. Images from Feulgen-stained sections from a clinical material of 197 tumours were analyzed. Features at various levels of analysis, e.g. mainly related to individual objects, neighbouring objects and the entire image, were analyzed. The features used were based on relational rather than individual nuclear features. With this technique, typical tissue architecture and degree of order/disorder can be described. These characteristics were compared by means of multivariate statistical methods with the subjective grading of the pathologists at our institution. This comparison provided the best subset of features and the agreement between the subjective and computer-based classification was 73%. The size, orientation and variation of the grey scale of the nuclei were particularly powerful. On a continuous scale, from grade 1 to 2A and 2B to 3, the four grades formed two distinct classes, low and high grade. In this distribution, the intermediate grade 2A was identified as a displaced grade 1 and the other intermediate grade 2B as a displaced grade 3.