Automatic Cell Counter Algorithm - Revision history

Vithoo: /* Pre-processing */

2018-09-04T07:46:11Z

Pre-processing

Vithoo: /* Pre-processing */

2018-09-04T07:45:35Z

Pre-processing

Vithoo: /* Picture Procedure */

2018-09-04T07:45:20Z

Picture Procedure

Vithoo: /* Picture Procedure */

2018-09-04T07:43:31Z

Picture Procedure

Vithoo: /* Picture Procedure */

2018-09-04T07:43:00Z

Picture Procedure

Vithoo: /* Picture Procedure */

2018-09-04T07:41:02Z

Picture Procedure

Vithoo: /* Picture Procedure */

2018-09-04T07:38:21Z

Picture Procedure

Vithoo: /* Picture Procedure */

2018-09-04T07:37:18Z

Picture Procedure

Vithoo at 07:35, 4 September 2018

2018-09-04T07:35:58Z

Vithoo at 15:25, 3 September 2018

2018-09-03T15:25:59Z

@@ Line 23: / Line 23: @@
 Several methods were tried to remove the background from the image of interest. First a simple subtraction of the background image was done. Unfortunately, this method results in strange horizontals lines which may be due to the actualisation of the camera. For some images it was not a problem but for others the cell was very difficult to detect due to those lines.
 Another method was then tested, the difference between the image representing the cell and the background image was computed. Then the cell is much more easily selected.
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@@ Line 22: / Line 22: @@
 ===Pre-processing===
-Then several methods were tried to remove the background from the image of interest. First a simple subtraction of the background image was done. Unfortunately, this method results in strange horizontals lines which may be due to the actualisation of the camera. For some images it was not a problem but for others the cell was very difficult to detect due to those lines.
+Several methods were tried to remove the background from the image of interest. First a simple subtraction of the background image was done. Unfortunately, this method results in strange horizontals lines which may be due to the actualisation of the camera. For some images it was not a problem but for others the cell was very difficult to detect due to those lines.
 Another method was then tested, mainly the difference between the image representing the cell and the background image was computed. Then the cell is much more easily selected.

@@ Line 11: / Line 11: @@
 First, we took photos while zooming on the cells of interest. As cells are quite translucent, they were difficult to detect. In addition, we realized that the microscope was so dirty that the durst was detected as well as the cells and it may be difficult to distinguish them. It was thus decided to apply some pre-processing instead of directly searching for cells contour.
-The pre-processing will mainly remove noise due to the difference in luminosity. In order to apply the background removal, we took a picture of the background without focusing on anything and compare it to the image of interest. The pre-processing would be easier if the field of view is the same on all images. Thus we thought it was better to take a picture of the whole field of view instead of zooming on the thing of interest.
+The pre-processing will mainly remove noise due to the difference in luminosity. In addition it will ignore the durst that is present in both images. In order to apply the background removal, we took a picture of the background without focusing on anything and compare it to the image of interest. The pre-processing is easier if the field of view is the same on all images (same luminosity). Thus we thought it was better to take a picture of the whole field of view instead of zooming on the thing of interest.
 <gallery perrow="4" mode="packed" widths="px" heights="px">

@@ Line 9: / Line 9: @@
 ==Picture Procedure ==
-First, we took photos while zooming on the cells of interest. As cells are quite translucent, they were difficult to detect. In addition, we realized that the microscope was so dirty that the durst was detected as well as the cells and it may be difficult to distinguish them. It was thus decided to apply some preprocessing instead of directly searching for cells contour.
+First, we took photos while zooming on the cells of interest. As cells are quite translucent, they were difficult to detect. In addition, we realized that the microscope was so dirty that the durst was detected as well as the cells and it may be difficult to distinguish them. It was thus decided to apply some pre-processing instead of directly searching for cells contour.
 The pre-processing will mainly remove noise due to the difference in luminosity. In order to apply the background removal, we took a picture of the background without focusing on anything and compare it to the image of interest. The pre-processing would be easier if the field of view is the same on all images. Thus we thought it was better to take a picture of the whole field of view instead of zooming on the thing of interest.

@@ Line 11: / Line 11: @@
 First, we took photos while zooming on the cells of interest. As cells are quite translucent, they were difficult to detect. In addition, we realized that the microscope was so dirty that the durst was detected as well as the cells and it may be difficult to distinguish them. It was thus decided to apply some preprocessing instead of directly searching for cells contour.
-In order to apply the background removal, we took a picture of the background without focusing on anything. The pre-processing will also remove noise due to the difference in luminosity. This removal would be easier if the field of view is the same on all images. Thus we thought it was better to take a picture of the whole field of view instead of zooming on the thing of interest.
+The pre-processing will mainly remove noise due to the difference in luminosity. In order to apply the background removal, we took a picture of the background without focusing on anything and compare it to the image of interest. The pre-processing would be easier if the field of view is the same on all images. Thus we thought it was better to take a picture of the whole field of view instead of zooming on the thing of interest.
 <gallery perrow="4" mode="packed" widths="px" heights="px">

@@ Line 9: / Line 9: @@
 ==Picture Procedure ==
-First, we took photos while zooming on the cells of interest. As cells are quite translucent, the cells were quite difficult to detect. In addition, we realized that the microscope was so dirty that the durst was detected as and it may be difficult to distinguish it from interesting things. It was thus decided to apply some preprocessing instead of directly searching for cells contour.
+First, we took photos while zooming on the cells of interest. As cells are quite translucent, they were difficult to detect. In addition, we realized that the microscope was so dirty that the durst was detected as and it may be difficult to distinguish it from interesting things. It was thus decided to apply some preprocessing instead of directly searching for cells contour.
 In order to apply the background removal, we took a picture of the background without focusing on anything. In order to remove also the noise due to the difference in luminosity, we took it was better to take a picture of the whole field of view.

← Older revision		Revision as of 07:35, 4 September 2018
Line 1:		Line 1:
−	The aim of this algorithm is first to detect cells (or groups of cells), to count them and to find cells containing a micronucleus. Theoretically this ~~would~~ be easy as the micronuclei ~~would also~~ be as coloured as the nucleus. But other elements, bacteria for instance, can also be coloured by the dye. The big deal seems to be to distinguish micronuclei from those other elements.	+	The aim of this algorithm is first to detect cells (or groups of cells), to count them and to find cells containing a micronucleus. Theoretically this may be easy as the micronuclei should be as coloured as the nucleus. But other elements, bacteria for instance, can also be coloured by the dye. The big deal seems to be able to distinguish micronuclei from those other elements.

	==Background and Material Used==		==Background and Material Used==

← Older revision		Revision as of 15:25, 3 September 2018
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	==Nucleus Detection==		==Nucleus Detection==
		+
		+	==Available Code==