System, method, and computer software for linked window interfaces
Systems, methods, and computer program products are described for providing a graphical user interface (GUI) that may include a first openable window of image features constituting, for example, a pseudo-image of a scanned probe array. The image features each have one or more characteristics representing one or more hybridization reactions associated with a probe of the probe array. The GUI also has a second openable window including data features, each relating to one or more quantifications of one or more hybridization reactions associated with a probe of the probe array. This second window may be, for example, a scatter plot of hybridization intensities of probes to two or more labeled samples. The GUI further includes a third openable window including descriptive features such as rows of a spreadsheet. Each row may include descriptive elements associated with a probe. When a user selects a feature from any of the two or more windows, a corresponding feature in at least one other of the two or more windows is highlighted.
1 . A user interface, comprising:
a first openable window having a plurality of first image features, each having one or more characteristics representing one or more hybridization reactions associated with a probe of a probe array;
a second openable window having a plurality of data features, each relating to one or more quantifications of one or more hybridization reactions associated with a probe of the probe array; and
a third openable window having a plurality of descriptive features, each including one or more descriptive elements associated with a probe of the probe array.
2 . The user interface of claim 1 , wherein the probe array comprises a spotted array.
3 . The user interface of claim 1 , wherein the probe array comprises a synthesized array.
4 . The user interface of claim 1 , wherein the first, second, and third openable windows are all open in the interface at a same time.
5 . The user interface of claim 1 , further comprising:
a fourth openable window having a plurality of second image features, each having one or more characteristics representing one or more hybridization reactions associated with a probe of the probe array.
6 . The user interface of claim 5 , wherein the first image features are generated based on emissions of a first wavelength and the second image features are generated based on emissions of a second wavelength different from the first wavelength.
7 . The user interface of claim 1 , wherein the one or more characteristics of the plurality of first image features include a chromatic value representing degree, efficiency, or intensity of hybridization.
8 . The user interface of claim 7 , wherein the chromatic value is a hue, brightness, lightness, or saturation value.
9 . The user interface of claim 1 , wherein the one or more characteristics of the plurality of first image features include an intensity value representing degree, efficiency, or intensity of hybridization.
10 . The user interface of claim 9 , wherein the intensity value includes a gray-scale value.
11 . The user interface of claim 1 , wherein:
the plurality of first image features comprises a pseudo-image of the array.
12 . The user interface of claim 1 , wherein the plurality of data features each represent a quantification of degree, efficiency, or intensity of hybridization of a probe based on the probe hybridizing with none, one or a plurality of targets.
13 . The user interface of claim 12 , wherein the second openable window comprises a two-dimensional scatter plot wherein the plurality of data features comprises marks on the scanner plot, each representing a quantification of degree, efficiency, or intensity of hybridization of a probe with first and second targets.
14 . The user interface of claim 12 , wherein the second openable window comprises a histogram wherein the plurality of data features comprises bars, each representing a quantification of a number of probes having in common a range of degree, efficiency, or intensity of hybridization with one or more targets.
15 . The user interface of claim 12 , wherein the second openable window comprises a graphical representation selected from the group consisting of a scatter plot, histogram, bar graph, or line graph.
16 . The user interface of claim 1 , wherein the plurality of descriptive features comprises rows of a spreadsheet wherein each row includes one or more descriptive elements associated with a probe.
17 . The user interface of claim 1 , wherein the descriptive elements comprise any one or more of the group of elements consisting of absolute image intensity value, relative image intensity value, user-supplied data related to the probe, biological information related to the probe; probe identifier, probe x-coordinate identifier, probe y-coordinate identifier, probe-related data, probe data links, pin identifier, well plate identifier.
18 . The user interface of claim 17 , wherein the probe data links include links to remotely or locally stored user-supplied data related to the probe or links to remotely or locally stored biological information related to the probe.
19 . The user interface of claim 17 , wherein the probe-related data include any one or more datum selected from the group consisting of chromosome location of a gene or EST represented by the probe, band location on the chromosome, or SNP or other marker identifying the location on the chromosome.
20 . The user interface of claim 1 , wherein when a user selects a first image feature associated with a first probe, a data feature or a descriptive feature associated with the first probe, or both, are highlighted.
21 . The user interface of claim 1 , wherein when a user selects a data feature associated with a first probe, a first image feature or a descriptive feature associated with the first probe, or both, are highlighted.
22 . The user interface of claim 1 , wherein:
when a user selects a descriptive feature associated with a first probe, a first image feature or a data feature associated with the first probe, or both, are highlighted.
23 . A user interface, comprising:
two or more windows selected from the group consisting of
a first window having a plurality of image features, each having one or more characteristics representing one or more hybridization reactions associated with a probe of a probe array;
a second window having a plurality of data features, each relating to one or more quantifications of one or more hybridization reactions associated with a probe of the probe array; and
a third window having a plurality of descriptive features, each including one or more descriptive elements associated with a probe of the probe array;
wherein, when a user selects a feature from any of the two or more windows, a corresponding feature in at least one other of the two or more windows is highlighted.
24 . A computer program product comprising:
(a) an image processor constructed and arranged to process image data based on scanning a probe array; and
(b) a GUI manager constructed and arranged to provide two or more windows selected from the group consisting of
(i) a first window having a plurality of image features based on the processed image data, each having one or more characteristics representing one or more hybridization reactions associated with a probe of the probe array,
(ii) a second window having a plurality of data features, each relating to one or more quantifications of one or more hybridization reactions associated with a probe of the probe array, and
(iii) a third window having a plurality of descriptive features, each including one or more descriptive elements associated with a probe of the probe array.
25 . The computer program product of claim 24 , wherein:
when a user selects a feature from any of the two or more windows, the GUI manager further is constructed and arranged to cause a corresponding feature in at least one other of the two or more windows to be highlighted.
26 . The computer program product of claim 24 , wherein the probe array is a spotted array.
27 . The computer program product of claim 24 , wherein the probe array is a synthesized array.
28 . A computer program product comprising:
a GUI manager constructed and arranged to provide two or more windows selected from the group consisting of
(i) a first window having a plurality of image features, each having one or more characteristics representing one or more hybridization reactions associated with a probe of a probe array,
(ii) a second window having a plurality of data features, each relating to one or more quantifications of one or more hybridization reactions associated with a probe of the probe array, and
(iii) a third window having a plurality of descriptive features, each including one or more descriptive elements associated with a probe of the probe array.
29 . A method comprising the steps of:
(a) providing image data based on scanning a probe array; and
(b) providing in a graphical user interface two or more windows selected from the group consisting of
(i) a first window having a plurality of image features based on the image data, each having one or more characteristics representing one or more hybridization reactions associated with a probe of a probe array,
(ii) a second window having a plurality of data features, each relating to one or more quantifications of one or more hybridization reactions associated with a probe of the probe array, and
(iii) a third window having a plurality of descriptive features, each including one or more descriptive elements associated with a probe of the probe array.
30 . The method of claim 29 , further comprising the steps of:
(c) receiving a user selection of a feature from any of the two or more windows; and
(d) causing a corresponding feature in at least one other of the two or more windows to be highlighted.
31 . A scanning system, comprising:
(a) a scanner constructed and arranged to scan a probe array to generate image data;
(b) an image processor constructed and arranged to process the image data; and
(c) a GUI manager constructed and arranged to provide two or more windows selected from the group consisting of
(i) a first window having a plurality of image features based on the processed image data, each having one or more characteristics representing one or more hybridization reactions associated with a probe of the probe array,
(ii) a second window having a plurality of data features, each relating to one or more quantifications of one or more hybridization reactions associated with a probe of the probe array, and
(iii) a third window having a plurality of descriptive features, each including one or more descriptive elements associated with a probe of the probe array.
32 . A scanning system, comprising:
a scanner constructed and arranged to scan a probe array to generate image data;
a computer; and
a computer program product that, when executed on the computer, performs a method comprising the steps of:
(a) processing the image data, and
(b) providing in a graphical user interface two or more windows selected from the group consisting of
(i) a first window having a plurality of image features based on the processed image data, each having one or more characteristics representing one or more hybridization reactions associated with a probe of a probe array,
(ii) a second window having a plurality of data features, each relating to one or more quantifications of one or more hybridization reactions associated with a probe of the probe array, and
(iii) a third window having a plurality of descriptive features, each including one or more descriptive elements associated with a probe of the probe array.
33 . The method of claim 32 , wherein:
the method performed by the computer program product further includes the steps of
(c) receiving a user selection of a feature from any of the two or more windows, and
(d) causing a corresponding feature in at least one other of the two or more windows to be highlighted.
34 . A computer system for providing a user interface with a scanner for scanning a probe array to generate image data, comprising:
a first window means for providing image feature means having one or more characteristics representing one or more hybridization reactions associated with probe means of the probe array;
a second window means for providing a data feature means related to one or more quantification means of one or more hybridization reactions associated with probe means of the probe array; and
a third window means for providing descriptive feature means including one or more descriptive elements associated with probe means of the probe array.
35 . A computer system for providing a user interface with a scanner for scanning a probe array, the system being programmed to display image features having one or more characteristics representing one or more hybridization reactions associated with a probe of the probe array, data features related to one or more quantifications of one or more hybridization reactions associated with a probe of the probe array, and descriptive features including one or more descriptive elements associated with a probe of the probe array.
36 . A computer program product comprising a GUI manager constructed and arranged to provide display regions for displaying image features representing hybridization associated with a probe of a probe array, data features related to quantifying the hybridization associated with a probe of the probe array, and descriptive features associated with a probe of the probe array.
37 . A computer program product comprising a GUI manager means for providing window means for displaying image feature means representing hybridization means associated with a probe means of a probe array, data feature means related to quantifying hybridization means associated with probe means of the probe array, and descriptive feature means associated with probe means of the probe array.