Title of Invention

"A METHOD FOR AUTOMATED MEASUREMENT OF MITOTIC ACTIVITY"

Abstract A method for automated measurement of mitotic activity, the method comprising using a microscope to obtain a magnified image of a histopathological specimen, using a camera to obtain digitized colour image data by photographing the magnified image and using computer apparatus to identify pixels in the image data having luminances associated with mitotic figures, select from among the identified pixels a reference pixel which is sufficiently close in position and luminance to another identified pixel to provide a reference colour, locate pixels in the image data with luminances sufficiently close to that of the reference colour to indicate potentially mitotic figures, increment image regions corresponding to potentially mitotic figures from the located pixels by adding pixels thereto, potential increments to image regions being implemented or rejected by according to whether or not their luminances are sufficiently close to respective image region luminances and sufficiently far from an image data background luminances and select grown image regions on the basis of thresholds for image region area, compactness and width/height ratio and count selected gown image regions as actually indicating mitotic figures on the basis of a threshold for number of such regions. Fig. 3
Full Text The present invention relates to a method for automated measurement of mitotic activity .
This invention relates to a method, an apparatus and a computer program for measurement of mitotic activity, which indicates cell division taking .place in a tissue specimen: it is particularly relevant to making measurements on potentially cancerous tissue such as breast cancer tissue. The method is also relevant to other forms of cancer such as colon and, cervical cancer.
Breast cancer is a common form of female cancer, and also occurs to a lesser extent in the male: once a lesion indicative of breast cancer has been detected, tissue samples are taken and examined by a histopathologist to establish a diagnosis, prognosis and treatment plan. However, pathological analysis of tissue samples is a time consuming and inaccurate process. It entails interpretation of images by human eye, which is highly subjective; it is characterised in particular by considerable subjectivity in observations of the same samples by different observers and even by the same observer at different times. For example, two different observers assessing the same ten tissue samples may give different opinions for three of the slides - 30% error. The problem is exacerbated by heterogeneity, i.e. complexity of some tissue sample features.
f
Published International Application No. WQ 02/47032 A1 relates to measurement of DNA in cells from cell Images to indicate mitotic phase. It refers to the use of other image • analysis parameters giving one example," magnitude of intensity variance, but does not give details of how this variance can be used to indicate mitotic activity.
There is a need to provide an objective form of measurement of mitotic activity to inform a pathologist's diagnosis and patient treatment.
In one aspect, the present invention provides a method of measuring mitotic activity from hlstopatholo'gical specimen image data, characterised in that the method has the steps of:
a) identifying pixels in the Image da'ta having luminances associated with mitotic figures;
b) selecting from among the identified pixels a reference pixel which is sufficiently close
in position and luminance to another identified pixel to provide a reference colour;
c) locating pixels in the image data with luminances sufficiently close to that of the
reference colour to indicate potentially mitotic figures;
d) incrementing image regions corresponding to potentially mitotic figures from the

located pixels by adding pixels thereto, potential increments' to image regions being
implemented or rejected' by according to whether or not their luminances are
sufficiently close to respective image region luminances and sufficiently far from an
image data background luminance;
e) selecting grown image regions on the basis of thresholds for image region area,
compactness and width/height ratio; and
f) counting selected grown image regions as actually indicating mitotic figures on the
basis of a thresholds for number of such regions.
The invention provides the advantage that it provides an objective measurement of mitotic
activity to inform a pathologist's diagnosis and patient treatment.
The step of selecting grown image regions may also involve thresholds for ratio of image
region luminance to background luminance and area difference between areas derived by
growing each image region with multiple thresholds. The thresholds for image region area,
compactness, width/height ratio, luminance and area difference may be: 355 pixels The step of counting selected grown image regions may also involve thresholds for region
area and luminance. Successive potential increments to image regions may be individual
pixels each of which is an immediate row or column neighbour of an existing image region
pixel. Step b) may implemented with a reference pixel having a luminance differing by less
than 8% compared to another identified pixel distant from it by not more than two percent
of a smaller of two image dimensions.
Step a) may include white balancing and median filtering the image data prior to
identifying pixels having luminances corresponding to mitotic figures. In step c) pixels may
be cued for acceptance or rejection as regards indicating mitotic figures by:
a) thresholding colour image data to remove pixels lacking intensities associated with
mitotic figure imagery,
b) removal pixels not present in all colours, and
c) thresholding image- region areas to remove those too small and too large to be
potential mitotic figures.
In step c) pixels may alternatively be cued for acceptance or rejection as regards
indicating mitotic figures by:
a) segmenting to identify pixels with intensities associated with mitotic figure imagery,
b) thresholding image region areas to remove those too small and too large to be
potential mitotic figures,
c) cluster analysis to determine whether or not a pixel's image region is in a sufficiently
large cluster, and
d) necrotic and hairy edge filtering.
In another aspect, the present invention provides a method of measuring mitotic activity
from histopathological specimen image data, characterised in that the method has the
steps of:
a) measuring an intensity profile of an image region corresponding to a potentially mitotic
figure,
b) counting the image region as indicating a mitotic figure if its profile has a value greater
than a prearranged threshold at a position in the profile having intensity associated
with mitotic figure imagery.
this aspect preferably includes counting the image region as indicating a mitotic figure if
its profile has a first value not greater than the prearranged threshold at a position in the
profile having intensity associated with mitotic figure imagery, a second value greater than
a prearranged second threshold, a third value greater than a prearranged third threshold,
and a minimum value less than a prearranged fourth threshold. The first value may be at
one end of the profile, the first and second values may adjoin one another in the profile
and the third value may not adjoin the second value.
The image data may comprise a first Principal Component obtained by Principal
Component Analysis (PCA) of coloured image data, and step a) may include
preprocessing image data by:
a) decomposing the image data into overlapping sub-images,
b) applying PCA to the sub-images to derive a first Principal Component image,
c) thresholding the first Principal Component image to produce a binary image of blobs
and background
d) rejecting blobs adjacent to or intersecting sub-image boundaries,
e) filling holes in blobs,
f) rejecting blobs too small to correspond to potential mitotic figures, and
g) reassembling the sub-images into a single image for image region profile
measurement as aforesaid in step a).
After step g) pixels may be cued for acceptance or rejection as regards indicating mitotic
figures by:
a) thresholding colour image data to remove pixels lacking intensities associated with
mitotic figure imagery,
b) removal pixels not present in all colours, and
c) thresholding image region areas to remove those too small and too large to be
potential mitotic figures.
After step g) pixels may alternatively be-cu'ed for acceptance or rejection as regards
indicating mitotic figures by:
a) segmenting to identify pixels with intensities associated with mitotic figure imagery,
b) thresholding image region areas to remove those tod small and too large to be
potential mitotic figures,
c) cluster analysis to determine whether or not a pixel's image region is in a sufficiently
large cluster, and
d) necrotic and hairy edge filtering.
In another aspect, the present invention provides computer apparatus for measuring
mitotic activity from histopathological specimen, image data, characterised in that it' is
programmed to execute the-steps of:
a) identifying pixels in the image data having luminances associated with mitotic figures;
b) selecting from among the identified pixels a reference pixel which is sufficiently close
i
in position and luminance to another identified pixel to provide a reference colour;-'
c) locating pixels in the image data with luminances sufficiently close to that of the
reference colour to indicate potentially mitotic figures;
d) incrementing image regions corresponding to potentially mitotic figures from the
located pixels by adding pixels thereto, potential increments to image regions being
implemented or rejected by according to whether or not their lumjnances are
sufficiently close-to respective image region luminances and sufficiently far from an
image data background luminance;
e) selecting grown image regions on the basis of thresholds for image region area,
compactness and width/height ratio; and
f) counting selected grown image regions as actually indicating mitotic figures on the
basis of a thresholds for number of such regions.
Computer apparatus for measuring mitotic activity from histopathological specimen image
data, characterised in that it is programmed to execute the steps of:
a) measuring an intensity profile of an image region corresponding to a potentially mitotic
figure,
b) counting the image region as indicating a mitotic figure if-its profile has a value greater
than a prearranged threshold at a position in the profile having intensity associated
with mitotic figure imagery.
In yet another aspect, the present invention provides a computer program for use in
measuring mitotic activity from histopathological specimen image data, characterised in
that the computer program contains instructions to control a computer to implement the
steps of:
a) identifying pixels in the image data having luminances associated with mitotic figures;
b) selecting from among the identified pixels a reference pixel which is sufficiently close
in position and luminance'to another identified pixel to provide a reference colour;
c) locating pixels in the image data with luminances sufficiently close to that of the
reference colour to indicate potentially mitotic figures;
d) incrementing image regions corresponding to potentially rnitotic figures from the
located pixels by adding pixels thereto, potential increments to image regions being
implemented or rejected by according to whether or' not their luminances are
sufficiently close-to respective imagerregion luminances and sufficiently far from an .
image data backgroundrltiminance;
e) selecting grown image regions on the basis of thresholds for image region area,
compactness and width/height ratio; and
f) counting selected grown image regions as actually indicating mitotic figures on the.
basis of a thresholds for number of such regions.
In an additional aspect, the present invention provides a computer program for use in
measuring mitotic activity fronrhistopathological specimen image data, characterised in
that its instructions provide for implementing the steps of:
a) measuring an intensity profile of an image region corresponding to a potentially mitotic
figure, and
b) counting the image region as indicating a mitotic figure if its profile has a value greater
than a prearranged threshold at a position in the profile having intensity associated
with mitotic figure imagery.
The computer apparatus and computer program aspects of the invention may have
preferred features equivalent to corresponding method aspects of the Invention.
In order that the invention might be more fully understood, embodiments thereof will now
be described, by way of example only, with reference to the accompanying drawings, in '
which:-
Figure 1 is a block diagram of a procedure for measuring mitosis activity of the
invention, and incorporating mitosis cueing, feature detection and counting;
Figure 2 shows in more detail mitosis cueing in the procedure of Figure 1;
Figures is a block diagram of an alternative approach to mitosis'cueing in the
procedure of Figure 1;
Figure 4 illustrates the use of hidden Markov random field segmentation in the Figure 3
mitosis cueing procedure;
1! ' I
Figures shows inLrn'6Ye"defail mitosis'"feature detection in the procedure of Figure 1;
and
Figure 6 is a block diagram of an alternative approach to mitosis feature detection in the
procedure of Figure 1.
Referring to Figure 1 j a procedure 10 for the assessment of tissue samples in the form of
histopathological slides of potential carcinomas of the breast is shown. This drawing
illustrates processes for measuring mitotic activity to produce a parameter for use by a
pathologist as the basis for assessing patient diagnosis.
The procedure 10 employs a database 12, which maintains digitised image data obtained
from histological slides as will be described later. Sections are taken (cut) from breast
tissue samples (biopsies) and placed on respective slides. Slides are stained using the
staining agent haematoxylin & eosin (H&E), which is a common stain for delineating tissue
and cellular structure. Tissue stained with H&E is used to assess mitotic activity.
Measurement of mitotic activity in a tissue specimen gives an indication of the degree of
cell division that is taking place. A histopathologlcal slide is a snap shot representing a
very short time interval in a cell division process, so the chance of such a slide showing a
particular phase of mitotic activity is very small: if such a phase is in fact present in a slide,
that is a good indicator of how fast a potential tumour is growing.
In a prior art manual procedure for scoring mitotic activity, a clinician.places'a slide under
a microscope and examines a region of it (referred to as a tile) at magnification of x40 for
indications of mitotic activity. This manual procedure involves a pathologist subjectively
and separately estimating unusual colour, size, shape and boundary definition of cells in
tissue sample. The values obtained in this way are combined by the pathologist to give a
single measurement for use in diagnosis. The process hereinafter described in this
example replaces the prior art manual procedure with an objective procedure.
The invention uses image data from histological slides. In the present example, image
data were obtained by a pathologist using Zeiss Axioskop microscope with a Jenoptiks
Progres 3012 digital camera. Image data from each slide is a set of digital images
obtained at a linear-magnification of 40 (i.e. 40X), each image being an electronic
equivalent of a tile.
To select images, a pathologist scans the microscope over a slide, and at 40X
magnification selects regions (tiles) of the slide which appear to be most promising in
terms of analysing of mitotic activity. Each of these regions is then photographed using the
microscope and digital camera referred to above, and this produces for each region a
respective digitised image in three colours, i.e. red, green and blue (R, G & B). Three
intensity values are obtained for each pixel in a pixel array to provide an image as a
combination of R, G and B image planes. This image data is stored temporarily at 12 for
later use. Ten digitised images are required for measurement of mitotic activity at 14
which then provides input to a diagnostic report at 28.
A number of alternative processes 16 to 24 will be described to measure mitotic activity in
a given sample: these comprise two alternative mitotic cueing processes 16 and-18 and
two alternative mitotic feature detection processes 20 and 24. The measure of mitotic
activity is converted at 26 into a mitotic count for use by a pathologist.
Referring now to Figure 2, the first alternative mitotic cueing process 16 is shown in more
detail. If it is selected for use, it is carried out for each of the ten digitised images
mentioned above, but will now be described for one such image referred to as the input
image. It is used to cue or identify dark image regions, which may correspond to mitotic
cells,
At a stage 30, from the input image three histograms are formed showing the occurrence
frequency of pixel intensities, one .histogram representing R (red) intensities, one B (blue)
and one G (green). For example, an image with 8 bits per colour per pixel would have a
histogram abscissa axis of 256 intensity values, 0 to 255, and a histogram ordinate axis of
number of pixels in the image having each intensity value. Each histogram is a vector
having 256 elements, and the ith element (i = 0 to 255) of each vector is the number of
pixels having intensity i in the R, G or B image plane.
The next stage is to threshold the R, G or B image planes at 32: to implement this, firstly
the total number NT of pixels in an image plane is counted (this will be the same value for
all three image planes). For each image plane NT is then divided by a respective empirical
R, G or B parameter PR, PQ or PB determined from experience of implementing the
invention: parameter values PR= 100, PQ = 100 and PB = 140 were derived manually and
empirically from a set of 250 test images obtained using the Zeiss Axioskop microscope
and Jenoptiks Progres 3012 camera mentioned above. Images produced using a different
microscope/camera combination might require different parameters. This procedure gives
three thresholds TR, TG and TB equal respectively to NT/PR, NT/PG and NT/PB.
The histograms' and the thresholds TR, TG and TB are then used for each image plane to
select low intensity pixels whose total number does not exceed the threshold TR, TG or TB.
So for example an image having a total number of pixels NT equal to 20,000 would have a
red and green image planes with PR= 100, PG = 100 and TR and TG equal to 200. For the
blue image plane TB is 2x104/140 or -142. in an eight-bit range of pixel intensities with
values 0 to 255, the red image plane histogram might have numbers of pixels 3, 20, 50, 7,
20, 80 and 65 at pixel intensity values 0 to 6 respectively. The total number of pixels
having pixel intensity values 0 to 6 is 245, which exceeds the red image plane threshold TR
of 200; however the total number over pixel intensity values 0 to 5 is less than 200, and
these are therefore retained and pixels with intensity values 6 to 255 are rejected. The
procedure retains a small part, of the histogram, which corresponds to the darker regions
of the red image plane (mitotic cells tend to be dark). This procedure is repeated for the
green and blue image planes using their respective thresholds. The objective is to retain in
each image plane a number of pixels which are likely to be in proportion to the number of
pixels in the image.
The next stage 34 is spatial filtering: here the red, green and blue retained pixels are
compared and every pixel which is not retained in all three image planes after thresholding
is rejected. Each pixel remaining after spatial filtering is then cued by assigning it a binary
1 value and all other pixels in the image which have rejected are set to binary 0: this
creates a single combined binary image for output from the stage 34.
At' 36, a technique known as "connected component labelling" (CCL) is applied to the
combined binary image from stage 34: this is a known image processing technique
(sometimes referred to as 'blob colouring') published by Klette R., Zamperoniu P.,
'Handbook of Image Processing Operators', John Wiley & Sons, 1996, and Rosenfeld A.,
Kak A.C., 'Digital Picture Processing', vols. 1 & 2, Academic Press, New York, 1982. CCL
gives numerical labels to image regions which are "blobs" in the binary image, blobs being
groups of contiguous or connected pixels of the same value 1 in a binary image containing
Os and 1s only: each group or blob is assigfied^a number (label) different to those of other
groups to enable individual blobs to be distinguished from others. CCL also provides blob
areas in terms of number of pixels.
Blobs are then-retained (pixels-set to -1;)1 or rejected (pixels set to 0) based on their
dimensions: blobs are retained, if they both contain from 95 to 5000 pixels inclusive and
have height and width'of not more-than 2000 pixels. In this example the minimum area of
95 pixels is deliberately set to a small value to avoid rejecting too many blobs that might
be of interest for possible mitotic activity. The maximum area is set to a large value for the
same reason. The output of stage 36 is a binary image containing a set of labelled blobs
for analysis for mitotic activity as will be described later. Stage 3& is useful for removing
blobs which aren't likely to be relevant for later processing, but it is not essential.
10
Referring now to Figure 3, the second mitotic cueing process 18 is shown in more detail.
As in the previous example, if the process 18 is selected for use, it is carried out for each
of the ten digitised images mentioned above, but will now be described for one such
image. At a stage 40 a single iteration of a technique known as "Hidden Markov Random
Field segmentation" is performed on the red component of an original (RGB) input image
of a tile. This segmentation is a known image processing technique, see by Devijver P.A.,
'Image segmentation using causal Markov Random Field models', Pattern Recognition,
J.Kittler (ed) Lecture Notes in Computer Science 301, Springer-Verlag 1988; also
Ducksbury P.G., 'Parallel model based segmentation using a 3rd order hidden Markov
model', 4th IEE Int. Conf. Image Processing and its Applications, Maastricht, 7-9 April,
1992. The input image is quantised into four levels (i.e. reduced from potentially 256 grey
levels to just four): the first of these levels corresponds to very dark areas of the input
image, second and third levels are progressively less dark and the fourth level
corresponds to light image areas. The input image's grey level histogram is computed and
initially fitted with a set of four Gaussian distributions of number of pixels N(x) as a
function of pixel value x, the distributions having a variety of means jx and standard
deviations a and each being of the form:-
In this example, the Equation (1) distributions form the basis of image segmentation,
which is defined as separation of objects from a background in a digital image. The
Gaussian distributions are numbered 1 to 4 respectively. If an image pixel has a grey level
that falls within Gaussian distribution number j (j = 1, 2, 3 or 4), then its segmented label is
j. However where there is overlap of Gaussians as in shaded areas in Figure 4 then the
power of the Markov segmentation algorithm comes into effect in making a probabilistic
decision as to which is the best segmented label to choose. The output from this stage 40
is a mask image where-each pixel has been allocated one of four numbers (1, 2, 3 or 4).
Only pixels having label' 1 (corresponding! to dark image areas) are used in subsequent
processing stages. Even though only label 1 pixels are retained, for good image
segmentation it is better to use'an adequate number of levels or labels (four in this case)
and to assign pixels correctly: this improves the results for label 1. Using too few
segmentation levels, segmented regions may be too large and contain inappropriate
pixels; with too many levels, segmented regions may be too small and fragmented.
Segmentation into four is found to be a good compromise, despite using only lowest
numbered pixels' in later processing. Stage 40 is a useful segmentation technique but
others can be used instead.
At 42 a K-means clustering process is performed: this is a known process which is
described by J.A. Hartigan and MA Wong in a paper entitled 'A K-means clustering
algorithm', Algorithm AS 136, Applied Statistics Journal, 1979. K-means is an iterative
statistical technique for computing an optimal set of clusters (groups of data items sharing
some common property) from a dataset. This process uses raw image pixels from the red
component of the original (RGB) input image of a tile input at 40: it selects those red pixels
that are located in the same image position as pixels labelled 1 in the mask image
generated at 40. Designating the maximum and minimum of the values of the label 1 raw
image pixels as "max" and "min" respectively, three clusters are used and initially cluster
centres for the K-means technique are set relative to the dynamic range (max - min) of
these pixels as follows:
Cluster
1
2
3
min + 0.1 x (maxmin
+ 0.5 x (max -
Initial
min)
min)
max -0.1 x(max-min)
cluster centre setting
10% of
middle
10% of
dynamic range above min
of dynamic range
dynamic range below max
From the result of the K-means technique-two masks are created: one mask marks areas
containing cluster 1 OR cluster 2 (the joint cluster mask) whilst the second mask marks
just cluster 1 in isolation (the cluster 1 mask). Only clusters 1 'and 2 are required for later
processing; the third cluster is used simply to separate data on a more reasonable basis.
At 44 connected component labelling (CCL, as previously described) is applied to the
mask created'at 42 which marks the joint cluster (cluster 1 OR cluster 2). CCL also gives
the areas of labelled blobs m-terms of numbers of pixels. Blobs that are outside an .allowed
area range are rejected, and those within this range are retained as indicated in the table
below and renumbered sequentially from label 1 upwards. The output from stage 44 is a
set of labelled blobs.
EITHER blob size size > 262144 pixels
70 pixels ^ blob size 12
Reject blob - set all its pixels to 0 and
exclude from set of labelled blobs
Accept for further processing and include
in set of labelled blobs
The maximum and minimum acceptable blob areas (262144 and 70 pixels) were chosen
to be sufficiently widely separated to avoid significant loss of potentially relevant blobs -
this dynamic range might be reducible if more knowledge of relevant blob sizes becomes
available. Stage 44 is useful to remove unwanted blobs but could be dispensed with.
At 46 each labelled blob generated at 44 is considered and accepted or rejected based on
a contextual analysis of its cluster 1/(cluster 1 + cluster 2) score; i.e. from the results of 42,
for each blob find how many of its pixels are in cluster 1 (NC1) and how many in cluster 2
(NC2): then calculate the ratio NC1/(NC1 + NC2), and accept the blob for further
processing if this ratio is 0.6 or greater. Reject the blob if the ratio is less than 0.6. The
result is a reduced set of blobs.
Contextual measure > cluster context threshold
(60%)
Contextual measure (60%)
Accept for further processing
into set of blobs
Reject blob
At 48 take the reduced set of blobs generated at 46 and perform a rejection using a
'necrotic filter': such a filter computes a standard metric referred to as the Euclidean metric
MEU of normalised quantised boundary phase (as described later). The Euclidean metric
MEU is of the form:
(2)
;'=!
where x\ andy/ (/= 1 to n) are elements of vectors x and y respectively representing the
two quantities to be compared. The 'necrotic filter' process is as follows: firstly, a Sobel
edge filter is applied to the labelled image obtained from step 44 and the raw image - i.e.
the red component of the original (RGB) input image input to stage 40 tile. The labelled
image is used to obtain the boundary of the blob that may correspond to a mitotic figure
and the rawlmage is used to obtain the phase angle of pixels in the raw image. Sobel is a
standard image processing technique published in Klette R., & Zamperoni P., 'Handbook
of image processing operators', John Wiley & Sons, 1995. A Sobel filter consists of two
3x3 arrays of numbers SP and SQ, each of which is convolved with successive 3x3 arrays
of pixels in an image. Here
A first 3x3 array of pixels is selected in the top left hand corner of the labeled image:
designating as Cg a general labelled pixel in row i and column j, the top left hand corner of
the image consists of pixels Cn to C13, C2i to C23 and C3i to C33. Cy is then multiplied by
the respective digit of SP located in the SP array as Cg is in the 3x3 cyan pixel array: i.e.
Cn to C13 are mutilplied by 1, 2 and 1 respectively, C2i to C23 by zeroes and C31 to C33 by -
1, -2 and -1 respectively. The products so formed are added algebraically and provide a
value p. The value of p will be relatively low for pixel values changing slowly between the
first and third rows either side of the row of Caa, and relatively' high for pixel values
changing rapidly between those rows: in consequence p provides an indication of edge
sharpness across rows. This procedure is repeated using the same pixel array but with
replacing SP) and a value q is obtained: q is relatively low for pixel values changing slowly
between the first and third columns either side of the column of C22, and relatively high for
pixel values changing rapidly between those columns, and q therefore provides an
indication of edge sharpness across columns. The square root of the sum of the squares
of p and q are then computed l.e.-^Jp2 + qz , which is defined as an "edge magnitude"-and
becomes T22 (replacing pixel C22 at the centre of the 3X3 array) in the transformed image.
Tan"1p/q is also obtained at each pixel and is defined as a "phase angle".
A general pixel Ty (row i, column j) in the transformed image is derived from CMJ.I to CHJ+II
Cy.-i to Cij+i and CM^ to CM^ of the labeled image. Because the central row and column
of the Sobel filters in Equation (3) respectively are zeros, and other coefficients are 1s and
2s, p and q for TU can be calculated as follows:
p = { CH.J-I + 2Cnj + CM,,,^} - { Cl+Ui + 2 C M ,j + CW,H} (4)
q = { Cn,j-i + 2Q.H + CW,,M} - { Cj.1ljf1 + 2C u+1 + C WJ+1 } (5)
Beginning with i = j = 2, p and q are calculated for successive 3X3 pixel arrays by
incrementing j by 1 and evaluating Equations (2) and (3) for each such array until the end
of a row is reached; j is then incremented by 1 and the procedure is repeated for a second
row and so on until the whole image has been transformed. The Sobel filter cannot
calculate values for pixels at image edges having no adjacent pixels on one or other of its
sides: i.e. in a pixel array having N rows and M columns, edge pixels are the top and
bottom rows and the first and last columns, or in the transformed image pixels TU to TIM,
TNI to TNM, TU to TIM and TIM to TNM- By convention in Sobel filtering these edge pixels are
set to zero. The output of the Sobel filter comprises two transformed images, one (the
edge filtered image) contains the boundaries of the labeled blobs produced at 44 whilst
the other contains the "phase angle" of the raw input image.
A pixel of a labelled blob is a boundary pixel if the like-located pixel in the Sobel edge
filtered image.is non-zero: for each boundary pixel the phase angle is extracted from the
like-located pixel in the .Sobel phase angle image. This phase angle information is then
quantised to reduce it to four orientation ranges (0 - 44, 45 - 89, 90 - 134, 135 - 179
degrees) and the number of boundary pixels in each orientation is normalised by dividing it
by the number of pixels in the perimeter of the blob. This results in a respective 4-element
vector of normalised orientations or quantised phase for each blob: The Euclidean
measure of each of these vectors is computed using Equation (2) and compared with that
of a perfect circle, in which the four vector elements are of equal value. This searches for
blobs relatively far from circularity. The Euclidean measures of the labelled blobs are
compared with a Euclidean Threshold of 0.4354 and are rejected if they are greater than
it. The Euclidean threshold was derived from a K-means analysis of a test dataset. Output
a set of remaining blobs.
Euclidean measure > 0.4354 Reject blob
Euclidean measure as 'part of a set of remaining blobs
At 50 each of the blobs remaining after step 48 is examined and a 'hairy edge filter'
operation is performed. A 'hairy edge filter' measures the amount of edge structure in an
area around a blob, this being a rough approximation to the 'hairy fibres' sometimes seen
around mitotic figures. This is computed for each blob as follows:
a) Two morphological dilations are applied using filters 5x5 and 13x13 pixels in size
as shown below.
0 0 1 0 0
0 1 1 1 0
5x5 filter = 1 1 1 1 1 (6)
1 1 1 1 0
0 0 1 0 0
0 0 0 0 0 0 1 0 0 0 0 0 0
0 0 0 1 1 1 1 1 1 1 0 0 0
0 0 1 1 1 1 1 1 1 1 1 0 0
0 1 1 1 1 1 1 1 1 1 1 1 0
0 1 1 1 1 1 1 1 1 1 1 1 0
0 1 1 1 1 1 1 1 1 1 1 1 0
13x13 filter = 1 1' 1 1 1 1 1 1 1 1 1 1 1 (7)
0 1 1 1 1 1 1 1 1 1 1 1 0
0 1 1 1 1 1 1 1 1 1 1 1 0
0 1 1 1 1 1 1 1 1 1 1 1 0
0 0 1 1 1 1 1 1 1 1 1 0 0
0 0 0 1 1 1 1 1 1 1 0 0 0
0 0 0 0 0 0 1 0 0 0 0 0 0
Morphological dilation is an expansion operation: for an original binary image (i.e. having
pixel values 1 and 0 only), the expansion operation comprises locating each pixel with
value 1 and setting pixels in its vicinity also to 1. In the two above arrays, a central 1
indicates a pixel found to be 1 in the image, other 1s indicate the relative positions of
nearby pixels set to 1 to implement morphological dilation, and Os represent pixels left
unchanged.
Morphology is an image processing technique based on shape and geometry. It is a
standard image processing procedure published in Umbaugh S.C., 'Colour vision and
image processing', Prentice Hall, 1998. Morphology applies a filter of some size and
shape to an image. In the simplest sense dilation (dilates (or expands) an object) at each
pixel position the output of the dilation is the logical OR of the inputs. The filters used
contain approximations to circles as shown above. The application of the two dilation
operations resujts in two dilated results. Each blob is dilated by two different amounts, as
described with reference to Equations (6) and (7): the blob resulting from the 5x5 filter is
then subtracted from that resulting from the 13x13 filter, which results in a border around
the blob. This is repeated for each of the blobs remaining after step 48.
b) A Sobel filter (as previously described) is applied to obtain the gradient'of the raw
image - i.e. the red component of the original (RGB) input image of a tile input at 40.
A summation of gradient values is formed within the area of the border (mask)
determined at a) around each blob and is used as a filter measure for comparison
with a Hairy Threshold for acceptance and rejection of blobs as shown in the table
immediately below.
Filter measure > Hairy Threshold
. (25000)
Accept blob as valid for processing for
mitotic feature detection
Filter measure (25000)
Reject blob
The output of step b) is a set of cued blobs considered valid for use in mitosis feature
detection as will be described later. Stages 46, 48 and 50 are desirable to reduce
unwanted blobs, but are not essential if the consequent processing burden in mitotic
feature detection can be tolerated.
Referring now to Figure 5, there is shown a flow diagram of the mitotic feature detection
process 20, which is carried out for each of the ten digitised input images referred to
above and will be described for one image. At a first stage 60, an input RGB image is
preferably white balanced by remapping its most luminous pixel to white. For each pixel /
(/= 1 to total number of pixels in image) in this image, pixel luminance L, is computed from
its red, green and blue intensities R/, G/ and B/ using the following equation:
L, = 0.299 X R / + 0.587 xG/ + 0.114xB, (8)
Then the pixel with the maximum of the luminance values of all pixels in the input (RGB)
image is located and used to record the corresponding values of R, G and B at that
maximum luminance pixel position and denoted LumMaxR, LumMaxG and LumMaxB. The
ratios for each of the three image planes are then computed as
RatioR = (255/LumMaxR) x 1.05 (9)
RatioG = (255/LumMaxG) x 1.05 (10)
RatioB = (255/LumMaxB) x 1.05- (11)
The original RGB pixel values are now multiplied by these ratios to produce a white
balanced image with three image planes with the following values for each pixel,/:
Balanced R, = R, x RatioR (12)
BalancedG, = G, x RatioG (13)
BalancedB,-= B, x RatioB . (14)
The final stage is to clip the new white balanced image so that no pixel values lie outside
the eight bit range (0 to 255). If any pixel value is less than 0, it is set to zero and if any
'pixel value is greater than 255, it is set to 255. Production of a white balanced image is
not essential but desirable to reduce variation between images.
At 62 the clipped white balanced image from step 60 is filtered with a 3x3 median filter to
remove spatial noise (desirable, but not essential). The filter is applied .independently to.
each of the balanced red (BalancedR), green (BalancedG) and blue' (BalancedB) image
planes computed at'60: the median filter operation selects each pixel in these image
planes in succession (other than edge pixels) and takes a 3 x 3 array of those pixels
centred on the selected pixel. The 3 x 3 array of pixels is then sorted into ascending order
of pixel value using what is referred to as."quicksort". Quicksort is a known technique
published by Klette R., Zamperoniu P., 'Handbook of Image Processing Operators', John
Wiley & Sons, 1996, and will not be described. It is not essential but convenient. The
median pixel value (fifth of nine) is then taken asjthe filter output to replace the value of
the selected pixel. This is repeated across the clipped white balanced image. Pixels in
edge rows and columns do not have the requisite 3x3 array, and for these the clipped
white balanced image pixel values are retained in the median filtered image.
At 64 an 'autopick colour' process is applied which picks or locates a pixel-having the
lowest luminance (darkest) in the median filtered image (excluding outlying pixels relatively
remote from pixels of similar luminance): this means that the chosen pixel has at least one
relatively nearby pixel with luminance similar to its own. Dark pixels are selected because
mitotic figures tend to have relatively low luminance using conventional histological slide
preparation techniques. The computation is as follows, for each pixel position in the
median filtered image the luminance L; is computed as follows:
L, = 0.299 XR, + 0,587 xG/ + 0.114 xB, (15)
Computing for each pixel position in the median filtered image using Equation (15)
provides a luminance image: in the luminance image a first pixel value and its location is
stored as a current .darkest pixel. Successive pixels in that image are compared with the
first pixel: if any .comparison pixel has L/ darker (lower value of luminance) than the current
darkest then its pixel value and its location are stored in a list of darkest pixels. After the
list has reached ten entries, the current least dark pixel in it is removed and replaced by a
later pixel on each occasion a later pixel is darker than the least dark pixel: this process
continues until all pixels have been compared with and where appropriate added to the
list. After processing the entire luminance image, the list of darkest pixels is sorted into
descending order of darkness using Quicksort (as mentioned above) so that the darkest is
first. If the procedure results in-less than ten darkest pixels, the stored comparison
luminance value originally obtained from the first pixel is increased and the procedure
repeated.
The next step is to determine whether or not the darkest pixel satisfies the condition that it
is located relatively near another of the ten darkest pixels: i.e. the condition is that these
two pixels be separated by a distance of not more than twenty pixels in any direction
(along a row, a column diagonally or between a diagonal and a row or column). This
condition applies to an image of dimensions 1476 pixels by 1160 pixels, so the maximum
separation is 2% of the smaller image dimension. If this condition is satisfied, a darkest
pixel has been located having a comparatively near neighbour of similar luminance and
therefore not considered to be an outlying pixel: the luminance of this darkest pixel is
denoted by. If the condition is not satisfied then the procedure is iterated by
discarding the current darkest pixel from the list and taking the remaining darkest pixel ;
iteration continues until the condition is met. The list size of ten was determined by
analysis of ,the ten images selected as previously described, but it is not critical and a
different number can be chosen. The pixel from which Lp^ed colour is taken should therefore
be selected from a small group (twenty or less) of the darkest pixels.
At 66 a 'colour proximity highlighting' is carried out which locates image pixels in the
median filtered image that have luminances differing from Lp^ad colour by less than 20 (i.e.
less than 8% for an eight-bit intensity range from 0 to 255). This is carried out by creating
a mask image as follows: for each pixel in the median filtered image, if a luminance
inequality condition (t6) below is true then the pixel is accepted and represented by a
value 255 in the equivalent position in the mask image.
| (0.299 x R; 4- 0.587 xG/ + 0.114 x B,) - (LpfcterfCDto) | If the inequality condition (16) is not true, then the current pixel is rejected and
represented by 0 in the mask image. Results from whichever of the cueing processes 16
and 18 has been used are introduced in this step 66: i.e. a pixel for which the inequality
condition (16) is true is accepted or rejected according .to whether there is a 1 or 0 value
respectively for a corresponding pixel located in the same position in the mitosis cued
. image resulting from process 16 or 18. It is not essential to use a process 16 or 18 but it is
useful to reduce processing burden.
At 68 accepted pixels are "grown" so that they come to correspond to a whole cell instead
of just part of a cell. Luminance proximity is used to check if growing should continue: i.e.
if the mask image computed at 66 indicates that there is too large a luminance difference
between a selected pixel and a test pixel as compared to a luminance difference threshold
denoted by LT (LT= 75 in this example),' growth with the selected pixel does not continue.
The process 68 of growing pixels is as follows: firstly, an image store labelled 'grow7 is
created that indicates whether pixel positions are 'grown' or 'not grown' and each entry or
pixel in 'grow' is initially set to 'false' (false = 0) indicating that no pixels have yet been
'grown': 'true' (true = 1) would indicate 'grown'. Secondly, a background colour for image
'grow' is computed from the median filtered image by averaging all pixels other than those
that are white (i.e. having R, G and B all equal to the maximum value of 255): the value of
this background colour is recorded. The growing process now proceeds in accordance
with the computer program steps below: in these steps a convention is used that an inset
of a line to the right indicates an iterative loop including the line and those following, it of
equal and greater inset, the loop terminating when a line of lesser inset is reached. .
For each pixel in the median filtered image:
If the mask image pixel is accepted and a corresponding pixel in the same location in
'grow' is 0 then:
Set the pixel in 'grow1 to true (1)
Enter the position of the pixel in 'grow' in a list entitled 'Action List'
As long as the Action List is not empty then:
Remove the most recently added pixel from the Action List but retain its
image position in memory and designate it as the 'removed pixel',
Select four pixels in 'grow' that are nearest neighbours of the removed
pixel, i.e. pixels immediately adjacent to'the removed pixel in the same
column or row only, not diagonal neighbours.
Select one of the nearest neighbour pixels not yet compared with
the mask image pixel,
If (and only if) the three following criteria are met, i.e. (a) the mask
image pixel and the selected nearest neighbour pixel differ in
luminance by less than LT, (b) the mask image pixel and the
background colour differ in luminance by more than LT, and (c) the
mask image pixel and a white pixel differ in luminance by more than
L, then:
Change from false (0) to true (1) the pixel in 'grow' located in
the same position as the selected nearest neighbour pixel, and
add the position of the selected nearest neighbour pixel to the
Action List
If any one or more of the criteria (a), (b) and (c) are not met, leave
the relevant pixel in 'grow1 unchanged and do not add its position to
the Action List
Repeat for next nearest neighbour pixel not yet compared with the
mask image pixel,
Repeat for next entry in the Action list
Repeat for all other mask image pixels.
The above computer program steps provide a mechanism for continuing to grow a cell
from an original single pixel in the mask image by reassessing further pixels for growth.
Nearest neighbour pixels of a 'seed' mask image pixel to be grown are assessed: each of
the nearest neighbours which becomes added (changed to 1) in growth is also added to
the Action List for its uncompared nearest neighbours to be assessed. Growth therefore
proceeds until all pixels adjoining but not part of a grown cell have been assessed and
have failed one or more of the three luminance criteria (a), (b) and (c). Growth then
terminates for that cell and restarts for another cell based on a new 'seed' mask image
pixel.
The result of 68 is a new image 'grow' which now contains a set of blobs (image regions of
contiguous pixels of value 1) which are candidates for indicating positions of real cells that
are likely to be of interest for mitosis. The blobs are processed at 70 by connected
component labelling as previously described: this derives a set of measurements for each
blob as follows:
area A (the number of pixels in a blob),
perimeter P (the number of pjxels on a blob's boundary),
compactness (4nAJP2),
width (maximum number of pixels in a row across a blob),
height (maximum number of pixels in a column down a blob),
ratio width/height,
luminance percentage: using median filtered image pixels located in the same
positions as the pixels of the blob, this measure is computed by multiplying by
100 the result of dividing the luminance of the darkest median filtered image
pixels by the luminance of the background colour,
perturbed difference (difference between grown blob sizes obtained using thresholds
corresponding to I_T perturbed by a prearranged increment and decrement
respectively), and
Hue difference (absolute value of difference between an average Hue and a
background Hue from the input image).
The perturbed difference is computed as follows:
the threshold LT is adjusted by adding a perturbation factor PF (PF=4) in this
example,
the growing process 68 is applied resulting in a new larger blob,
the threshold LT is adjusted by subtracting the perturbation factor PF, and
the growing process 68 is applied resulting in a new smaller blob,
A logical EXOR function is then computed between the new larger and smaller blobs: i.e.
each pixel in the smaller blob is EXORed with a respective pixel in the same position in the
larger blob. Outer pixels of the larger blob for which there are no like-located pixels in the
small blob are treated as being EXORed with a different pixel value. The EXOR function
yields a 1 for a pair of pixels of different value and a 0 for a pair of pixels of the same
value. Its results provide an EXOR image with each EXOR value located as'a pixel in the
same position as the blob pixels giving rise to it. The number of pixels equal to 1 in the
EXOR image is then counted and this number is the perturbed difference.
The Hue difference is' obtained for each blob as follows: the average colour of the median
filtered image pixels located in the same positions as the pixels of the blob is computed.
This average colour and the background pixel colour obtained earlier are then converted
from red/green/blue (RGB) to a different image space hue/saturation/value (HSV). The
RGB to HSV transformation is described by K. Jack in 'Video Demystified', 2nd ed.,
HighText Publications, San Diego, 1996. In this example the V and S components are not
required. H is calculated for the average colour of each blob and the background pixel
colour as follows:
Let M = maximum of (R,G,B) (17)
Let m = minimum of (R,G,B) (18)
Then
newr = (M - R)/(M - m)
newg = (M-G)/(M-m)
newb = (M - B)/(M - m)
Hue (H) then given by:
If R equals M then H = 60(newb - newg)
If G.equals M then H = 60(2 + newr - newb)
If B equals M then H = 60(4 + newg - newr)
If H greater than or equal 360 then H = H - 360
If H less than 0 then H = H + 360
(19)
(20)
(21)
(22)
(23)
(24)
(25)
(26)
The difference between the H values of the average colour of the median filtered image
pixels in the blob and the background pixel is then calculated for each blob and becomes
designated as the Hue difference for that blob.
If a blob's parameters satisfy all the conditions in the table immediately below then the
blob is accepted for further processing, otherwise it is rejected (deleted) by setting all its
pixels to 0.
Parameters for Accepted Blobs
355 pixels 0.17 Ratio of width/height Luminance percentage Perturbed difference Hue difference > 0
In the present example, the Hue difference will virtually always be true (due to the zero
threshold in the table immediately above). However in some circumstances it may be
desirable to have a non-zero threshold. Luminance percentage, perturbed difference and
Hue difference are not essential, and can be omitted from the thresholds in the table
above governing further processing or otherwise.
At 72 a two -quicksorts (as previously defined) are applied to the blobs to sort them into
two lists, one of blobs in ascending order of blob area and the other of blobs iri ascending
order of blob luminance in the median filtered image. The blobs in the two lists are now
referred to in accordance with groupings that they mark the end of: i.e. a blob is referred
to as the "darkest X% blob" to indicate that it together with blobs (if any) of lower
luminance than it are X% of the total number of blobs. Similarly, a blob is referred to as
the "largest Y% blob" to indicate that it together with blobs (if any) of greater area than it
are Y% of the total number of blobs.
A blob of median area (the "median blob", central in the area list) is now identified. If there
is an even number of blobs in the area list, the average area of the two central.blobs is
taken as the median area. Also at 72, unwanted blobs are eliminated to leave those
assessed as corresponding to mitotic figures as follows: if more than A blobs are present
and the largest blob is more than B percent of th'e area of the median blob, we retain each
of the largest C blobs which has a luminance not greater than that of the darkest D
percent blob. Otherwise, if the largest blob is not more than B percent of the area of the
median blob, retain each of the darkest £ blobs which has an area less than or equal the
largest Fpercent blob. In this example, values for A, B, C, D, E and Fare A = 2 blobs, B
= 200 percent, C= 3 blobs, D = 30 percent, E= 2 blobs, F= 80 percent. The process 72
is computed as follows:
If the number of blobs is less than or equal to A then accept each blob as being a mitotic
figure, the mitotic figure count is A and processing the current image terminates.
Otherwise, if the number of blobs is greater than A:
obtain area of largest blob,
obtain area of median blob,
if the largest blob area is more than B percent of the median blob area, then:
obtain the luminance of the darkest D percent blob - if there is no blob at a
Q percent position take the luminance of a blob which is both darker and
nearest to a notional D percent blob position in the luminance list,
for each of the largest C blobs,
if blob luminance is less than or equal to the darkest D percent blob,
accept the blob as being a detected mitotic figure,
increase a count of mitotic figures by 1, and
repeat for remainder of largest C blobs until none remain
unassessed and output count of mitotic figures.
Otherwise, if largest blob area is not more than B percent of median blob area,
obtain the area of the largest F percent blob - if there is no blob at an F
percent position take the area of a blob which is nearest (in area) to a
notional F percent blob position in the area list,
For each of the darkest E blobs
if blob area is less than or equal to area of the largest F percent
blob,
accept the blob as being a detected mitotic figure, and
increase a count of mitotic figures (initially 0) by 1,
repeat for remainder of the largest E blobs until none remain
unassessed and output count of mitotic figures.
The criterion number of blobs is not greater than A may be the only one used if desired,
the mitotic count being taken as zero if this is not satisfied. The "otherwise" criterion, i.e.
number of blobs greater than A and subsequent criteria, provide a further option.
As previously mentioned, the process 2Q,.is carried out for a total of ten images or tiles:
this repetition is to increase the likelihood of observing mitotic activity. The mitotic counts
for the ten images are then added together to provide a sum which is converted to a
mitotic activity grading as will be described later.
Referring now to Figure 6, there is shown a flow diagram of an alternative mitotic feature
detection process 24 which is carried out for each of the ten digitised images mentioned
above. Although it is possible to use the whole image, at 120 the digitised image
(hereinafter the "input image") is for convenience separated into overlapping windows of
size 128x128 pixels. The windows overlap with 64 pixels in both horizontal and vertical
directions. Thus, each window overlaps half of its preceding window above and to the left
(if available). In each window Principal Component Analysis (PCA, Karhunen-Loeve
Transform) is applied. PCA is a standard mathematical technique described by Jollie I.T.,
'Principal Component Analysis', Springer series in statistics, Springer Verlag, 1986. It is
also described by Jackson J.E., 'A User Guide to Principal Compon.ents' pp 1-25, John
Wiley & Sons, 1991. PCA is a technique for transforming a set of (possibly correlated)
variables into a smaller number of uncorrelated variables called principal components. The
first principal component accounts for as much of the variability in the set of variables as
possible as compared to the other components: because of this it can be superior to
taking a red, green or blue image plane or an average thereof, which are also options at
this stage. PCA involves obtaining a covariance matrix of the set of variables and solving
for its eigenvalues and eigenvectors. The covariance matrix is calculated using the
formula
where Cy is the covariance of variable /with variable j, xk and y/f are the ith and jth feature
values of the kth object, jux is the mean of all N values of XK, fty is the mean of all .N values
of yk. The covariance matrix is 3x3 and PCA yields three eigenvectors: the eigenvectors
are treated as a 3x3 matrix, which is used to multiply the transpose of the Nx3 image
matrix to produce a product matrix. Trie product matrix has an Nx1 first column which is
the first principal component,-which may be considered as the most important component.
It is the component with the maximum eigenvalue, and it provides a greyscale sub-image
(one pixel value for each of N-pixels) with-;a maximum range of information compared to
equivalents associated with-other components. PCA is carried out for each of the
overlapping windows defined above and each provides a respective first principal
component and greyscale sub-image of size 128x128 pixels.
At 122, each sub-image resulting from 120 is converted to a corresponding binary subimage
by applying a thresholding method referred to as "Otsu". Otsu is a standard
thresholding technique published by Otsu N., 'A thresholding selection method from grey
level-histograms', IEEE Trans Systems, Man & Cybernetics, vol. 9, 1979, pp 62-66. The
Otsu threshold selection method aims to minimise for two classes a ratio of between-class
variance to within-class variance: i.e. the higher the variance between classes the better
the separation. In the present example the two classes are a below-threshold class (pixel
value 0) and an above-threshold class (pixel value 1), so by applying Otsu thresholding
the greyscale sub-image is converted into a binary sub-image containing a set of blobs.
At 124 all blobs (objects) that touch or intersect sub-image boundaries are removed. Thus,
if at any pixel a blob meets a border it is removed by setting its pixels to a background
pixel value. This is because such boundaries give blobs meeting them artificial straight
edges which can give misleading results later. Because of sub-image overlap, a blob
which appears partly in one image may appear wholly in another sub-image. This step 124
only arises from the use of sub-images.
At 126 the outputs from 124 are inverted and connected component labelling (CCL, as
described earlier) is applied in order to enable any holes in the blobs to be removed. This
is not essential, but it provides spatial filtering which improves results somewhat. Because
of the inversion, areas of pixel value 1 labelled by CCL labelling will be background pixels
and holes within blobs. Holes, i.e. all labelled areas other than background pixels, are
removed (filled in) by setting pixels of holes in each blob to the value of the blob's other
pixels.
At 128 the' outputs from 126 are inverted once more and CCL is applied: after this
inversion, the labelled areas are the blobs within the sub-image filled at 126. CCL also
yields blob centre positions used later. Any blobs smaller than a minimum area threshold
of 400 pixels are rejected, i.e. set to an image background value, in accordance with the
table immediately below. This is another desirable but not essential spatial filtering step.
Blob size min area (400 pixels)
Otherwise
Reject blob
Accept for further processing
labelled blobs
into set of
At 130 multiple sub-images output at 128 are reassembled into a new binary image which
28
is the same size as the original before decomposition at 120; the new binary image has
undergone filtering and now contains only blobs that are of interest for subsequent mitosis
processing. Image preprocessing terminates with step 130: the set of blobs remaining has
been cleared both of unwanted small blobs and of holes within blobs. Image
preprocessing using steps 120-130 is advantageous because it does not significantly
affect shapes of blob perimeters, which is important for mitosis analysis. Results from
whichever of the mitosis cueing processes 16 and 18 has been used are introduced in this
step 130: i.e. a blob is accepted or rejected according to whether or not there is a blob in
the mitosis cued image in substantially the same position (this could be implemented
using a logical AND operation). It is not essential to use a process 16 or 18 here but it is
useful to reduce'processing burden.
At 132 Principal Component Analysis (PCA, as previously described) is applied to the
entire input (RGB) image. As before, a. red, green or blue image plane or an average
thereof could be used, but PCA is preferred. PCA yields a first component which is a
greyscale image with a better information range than those of other components. A
feature extraction procedure 134 is applied to a local window of 51x51 pixels centered on
the centres of each of the blobs identified in pre-processing at 130 and appearing in the
greyscale image. The procedure 134 determines an average cross-section (profile) for
that respective region of the greyscale image that corresponds to each blob: for the
purposes of this calculation each grayscale value used is normalised to lie in the range 0
to 1 by dividing it by 255. A respective series of profiles of each blob is taken using a line
fifty-one pixels long .extending across the respective greyscale image region
corresponding to that blob and centered on the blob centre: this gives fifty-one pixel values
or histogram points per profile, and profiles are taken at nine different angular orientations
at 20 degree intervals: the respective mean of the nine profiles of each blob is' then
calculated.
A respective histogram of each mean profile is then obtained and quantised to just five
intervals or bins 1 to 5 as follows, (1) 0 (3) 0.4 centres at 0.1, 0. the mean profile having its respective intensity value: because this number is averaged,
over the nine profiles it need not be an integer. Bin 1 corresponds to a darkest group of
image intensity values, i.e. low greyscale values of the kind one would associate with
images of mitotic figures; mitotic figures are normally dark using conventional staining
techniques so relatively darker degrees of grey level are of more interest, bins 2 to 4
correspond to progressively brighter values and bin 5 to the brightest of the five values.
These are relative though because the profiles all come from relatively dark image
regions. An approximate mean profile is represented by five values each of which is an
intensity value in a respective bin averaged over nine measured profiles. Each set of five
values characterises a blob now treated as indicating an actual cell. The minimum value of
each mean profile is recorded as the variable 'minprofile', this being the contents (number
of pixels averaged over nine profiles) of the bin having the smallest contents of all five
bins.
At 136 the contents of bins 1, 2 and 4 are used to determine if a current cell that
corresponds to a current blob is mitotic or not. Specifically, the following criteria are
applied for each blob, where "bin (n)" means the contents of the nth bin and n = 1, 2 or 4:
If bin (1)> 7.6, then:
current cell is mitotic.
Otherwise, if bin (1) if bin (2) > 25.5 and bin (4) > 0 and minprofile current cell is mitotic
otherwise, i.e. if bin (2) 0.15) then
current cell is not mitotic
The first criterion - bin (1) > 7.6 - may.if desired be the only one used to determine
whether a cell is mitotic. The " otherwise " criterion - bin (1) Each alternative mitotic feature detection technique 20 and 24 produces measurements
derived from ten images. Each mitotic feature detection technique is applied to ten images
or tiles as has been said: the mitotic figures are counted for each image and the counts
are added together to provide a total for the ten images. The mitotic figure count for a
technique is low, medium or high with points 1, 2 or 3 according to whether it is 0 to 5, 6 to
10 or 11 or more respectively as shown in the table below.
Measurement: Number of
Mitotic figures in Ten Images
0-5
6-10
£11
Meaning
Low
Moderate
High
Points
1
2
3
The measurement of mitosis may be combined with others obtained for pleomorphism and
tubules by different methods to derive an overall grading referred to in medicine as a
"Bloom and Richardson grading": it is used by clinicians as a measure of cancer status.
The examples given in the foregoing description for calculating intermediate quantities and
results can clearly be evaluated by an appropriate computer program recorded on a
carrier medium and running on a conventional computer system. Examples of program
steps haven been given. Such a program is straightforward for a skilled programmer to
implement without requiring invention, because the procedures are well known. Such a
program and system will therefore not be described further.

We claim:
1. A method for automated measurement of mitotic activity, the method
comprising:
a) using a microscope to obtain a magnified image of a
histopathological specimen:
b) using a camera to obtain digitized colour image data by
photographing the magnified image; and
c) using computer apparatus to:
i. identify pixels in the image data having luminances
associated with mitotic figures;
ii. select from among the identified pixels a reference pixel which is sufficiently close in position and luminance to another identified pixel to provide a reference colour; iii. locate pixels in the image data with luminances sufficiently close to that of the reference colour to indicate potentially mitotic figures;
iv. increment image regions corresponding to potentially mitotic figures from the located pixels by adding pixels thereto, potential increments to image regions being implemented or rejected by according to whether or not their luminances are sufficiently close to respective image region luminances and sufficiently far from an image data background luminances; and v. select grown image regions on the basis of thresholds for image
region area, compactness and width/height ratio; and vi. count selected gown image regions as actually indicating mitotic figures on the basis of a threshold for number of such regions.
2. A method as claimed in Claim 1 wherein the thresholds for image region
area, compactness, width/height ratio, luminance and area difference
are: 355 pixels

Documents:

2055-DELNP-2005-Abstract-(25-05-2009).pdf

2055-DELNP-2005-Abstract-21-05-2008.pdf

2055-delnp-2005-abstract.pdf

2055-DELNP-2005-Claims-(25-05-2009).pdf

2055-DELNP-2005-Claims-21-05-2008.pdf

2055-delnp-2005-claims.pdf

2055-delnp-2005-complete specification (granted).pdf

2055-DELNP-2005-Correspondence-Others-21-05-2008.pdf

2055-delnp-2005-correspondence-others.pdf

2055-DELNP-2005-Description (Complete)-(25-05-2009).pdf

2055-delnp-2005-description (complete)-21-05-2008.pdf

2055-delnp-2005-description (complete).pdf

2055-DELNP-2005-Drawings-21-05-2008.pdf

2055-delnp-2005-drawings.pdf

2055-DELNP-2005-Form-1-(25-05-2009).pdf

2055-DELNP-2005-Form-1-21-05-2008.pdf

2055-delnp-2005-form-1.pdf

2055-delnp-2005-form-18.pdf

2055-DELNP-2005-Form-2-(25-05-2009).pdf

2055-DELNP-2005-Form-2-21-05-2008.pdf

2055-delnp-2005-form-2.pdf

2055-DELNP-2005-Form-3-21-05-2008.pdf

2055-delnp-2005-form-3.pdf

2055-delnp-2005-form-5.pdf

2055-DELNP-2005-GPA-21-05-2008.pdf

2055-delnp-2005-gpa.pdf

2055-delnp-2005-pct-206.pdf

2055-delnp-2005-pct-304.pdf

2055-DELNP-2005-Petition-137-21-05-2008.pdf

2055-DELNP-2005-Petition-138-21-05-2008.pdf

abstract.jpg


Patent Number 235006
Indian Patent Application Number 2055/DELNP/2005
PG Journal Number 31/2009
Publication Date 31-Jul-2009
Grant Date 24-Jun-2009
Date of Filing 13-May-2005
Name of Patentee QINETIQ LIMITED
Applicant Address REGISTERED OFFICE, 85 BUCKINGHAM GATE, LONDON SW1E 6PD, GREAT BRITAIN.
Inventors:
# Inventor's Name Inventor's Address
1 MARGARET JAI VARGA QINETIQ MALVERN TECHNOLOGY CENTER, E BUILDING ROOM 302, ST. ANDREWS ROAD MALVERN, WORCS WR14 3PS, ENGLAND.
2 CHRISTELLE MARIE GUITTET QINETIQ LIMITED, MALVERN TECHNOLOGY CENTRE, E BUILDING ROOM 304, ST.ANDREWS ROAD, MALVERN, WORCESTERSHIRE WR14 3PS, ENGLAND.
3 PAUL GERARD DUCKBURY QINETIQ LIMITED, MALVERN TECHNOLOGY CENTRE, E BUILDING ROOM 311, ST.ANDREWS ROAD, MALVERN, WORCESTERSHIRE WR14 3PS, ENGLAND
4 MARIA PETROU ELECTRONICS COMPUTING AND MATHEMATICS, UNIVERRSITY OF SURRY, GUILDFORD GU2 7XH, ENGLAND.
5 ANASTASIOS KESIDIS SEVASTOPOULOU 25, 11524 ATHENS, GREECE.
6 ROBERTO CIPOLLA DEPARTMENT OF ENGINEERING, FALLSIDE LABORATORY, ROOM 435, TRUMPINGTON STREET, UNIVERSITY OF CAMBRIDGE, CAMBRIDGE CB2 1PZ, ENGLAND.
PCT International Classification Number G06K 9/00
PCT International Application Number PCT/GB2003/004916
PCT International Filing date 2003-11-13
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 0226787.0 2002-11-18 U.K.