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Pixcavator releases

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See also History of Pixcavator.

This page will list all releases of Pixcavator. The first digit in the version number refers to the number of years of development since the start.

1 2010

1.1 Version 5.1

April 24, 2010

This release is primarily about fixing a few annoying bugs:

  • Loading image of sizes >2000x2000 causes the software to stall (fixed, but still impractical for processing).
  • Changing the color channels after processing causes messed up data in the Output tab.
  • Summary in the Output tab isn’t updated when manually select/deselect objects.
  • Some image processing tools in the Tools tab don’t work properly.

1.2 Version 5.0

January 31, 2010

New features, etc:

  • Your choice of settings in the Output tab (the position of the sliders) is preserved when you load a new image to analyze.
  • Your choice of color channels in the Analysis tab is preserved when you load a new image to analyze. With these two the user can apply the same settings to a sequence of images if they are similar in nature. So, we get as close as possible to bulk processing without actually creating this complex feature.
  • Luminosity is a new color channel that you can choose. It is computed as a combination of the red, green, and blue values: 0.299*R + 0.587*G + 0.114*B. There are four channels now.
  • "Display channel" is a new option in the Analysis tab (just like the one in the Output tab). If you have chosen to shrink the image, the shrunken version is shown. This way you can preview all channels and decide which is the best - before committing to time consuming analysis.
  • The "Help" menu provides now the links to the help pages of this wiki. The user's guide and the license are still provided with the program; they are to be found in the "Pixcavator" folder on your hard disk.
  • The actual processing time is shown when it's done, and a beep is produced - but only if processing has taken more than 5 seconds.
  • Up to 2000 contours are now shown on the image and their statistics is also displayed. When there are more than 2000 contours, neither is shown.
  • A few bugs have been fixed, some remain.

2 2009

2.1 Version 4.3

December 13, 2009

The update will help the user to create better image analysis reports with Excel.

Membrane original.jpg

These reports are based on the data in Pixcavator's output table that lists all objects in the image as well as their measurements and locations. The table, combined with the analysis settings, the statistical summary, and the frequencies of the values in the table, can be saved to hard disk in the form of a spreadsheet. This spreadsheet is a complete report of what has happened.

The frequencies allow one to create a histogram for each column, such as the size, to graphically illustrate the distribution of the values. One can also add images, format the text, etc. The end result may look like this:

Membrane excel modified.jpg

For more details read Report generation.

2.2 Version 4.2

June 10, 2009

In addition to a few minor improvements, the main novelty is more ways to change the analysis settings. There are six sliders now.

UGss-sliders.jpg

As before we have two sliders for the two main measurements – size and Contrast. Now, the confusingly named “Max growth rate” has been remade into Border contrast". What does it mean? Both this and the second slider consider the difference in intensity inside the object from that of the surrounding area. But, while the contrast slider considers the maximal difference throughout the object (that why it’s now called Max contrast), the border contrast slider looks at the area just inside the contour. The result is about the same as before: it detects sharp edges, i.e. the contours with the largest difference between what’s just inside and what’s just onside of it.

Gradient00(v40)1x 25 10 0.jpg Gradient00(v40)1x 25 10 15.jpg

The next slider works similarly but takes into account the average difference in intensity inside the object from that of the surrounding area. It’s called Average contrast.

The last two sliders simply thresholding the image. For example, if you set Intensity, dark to 100, the contours of dark objects will the intensity equal to exactly 100. If you set Intensity, light to 100, the contours of light objects will the intensity equal to exactly 155 (here 155=255-100). It was set this way in order to ensure that contours grow as you move any of the six sliders from left to right. This is a very unsophisticated tool but it’s quite effective when the image lighting is uniform.

The need for introducing these new tools came from a specific, real life image analysis task: Measuring staining in the liver.

2.3 Version 4.1

May 13, 2009

This version Pixcavator has only one new feature: the analysis is precomputed. The result is that moving sliders produces immediate effect on the contours and finding the best contours becomes very quick. You can see the effect in this video. The automatic stage of analysis is however quite longer than in the previous versions. That's why this is just a test release.

2.4 Version 4.0

April 17, 2009

First, an annoying bug in the user interface was fixed. A few minor bugs were fixed too.

Second, a new slider “Border contrast” replaces the old. The idea is that by moving it you can jump to the nest sharp border. For example in the image below, the change in the gray level is very gradual. So, if you move the slider “Size” or “Contrast”, the growth is very slow and the former won’t even notice the sharp edge. With the new slider you get there is just a few abrupt steps: border contrast = 0, 10, and 15, respectively.

Gradient00(v40)1x 25 10 0.jpg Gradient00(v40)1x 25 10 10.jpg Gradient00(v40)1x 25 10 15.jpg


3 2008

3.1 Version 3.3

December 13, 2008

First, a feature was added to help with image exploration. As you move the mouse around the analyzed image, the object you hover over is highlighted. The contour is shown blue and, if "Color objects" is chosen, the whole object is colored. The data about it is displayed under the image as before.

Hover.jpg

Second, the limitations on the kind of objects to be captured have been removed. To avoid dealing with excessive number of objects in the image and the spreadsheet, only objects with saliency above a certain threshold were taken into account and displayed. There have been no complaints about that until recently. A manufacturing company needs to analyze an 1000x2000 image which is almost all black with a few light dots here and there (1-3 pixels in size). In the new version even objects this small will be captured. However, the number of objects will be limited to 1000.

3.2 Version 3.2

December 1, 2008

Pixcavator was initially intended primarily for counting: cells, objects, and other features. Everything is designed around this task: the clickable contours, the spreadsheet, the averages of the measurements, etc. Now, more and more often we see Pixcavator used for measuring. The reason is simple. Manually measuring the area, or perimeter, of a complex object is close to impossible even if the image is clear and the object is has well defined borders. A medical example is here and another one here.

Drusen2.jpg Melanoma-brown.jpg Measuring.jpg Meat2.jpg Bee brood2.JPG

Pixcavator captures contours of all objects – light and dark - and displays all their measurements. If, however, there is just one object but with a few holes, it is important to see that this data gives you the area of what’s inside the contour. What you frequently need instead is the area of the object, which is

the area of what’s inside the contour - the areas of the holes.

UGss-review.jpg

The main new feature in version 3.2 is a step in that direction. Pixcavator now displays the two numbers above - the total area of dark and the total area of light – as percentages of the total size of the image (under Review summary, second row). So, to find the area of a dark object with light holes in it, one has to subtract these two numbers. (Caution: You have to make sure however that the holes are in the object not the background).


3.3 Version 3.1

August 14, 2008

The updated interface is the first thing that you notice. All buttons and sliders are arranged in groups accompanied by headers. Text and tooltips were improved throughout.

Ss31small.jpg

The RGB channel analysis was completed to include all three channels. Just click a button in the Analysis tab for the color you want.

A new, “Max growth rate”, slider was introduced. Let me explain what it is. As you may remember, object in the image are allowed to grow – from one level of gray to the next - up to the extent set by the slider. For example, the object will grow until it’s both larger than say 100 pixels and has contrast above 20. Now, this is a totally different kind of slider. If you choose 10, the object will be allowed to expand – from one level of gray to the next - as long as its size grows by 10% or less. Roughly, the expansion stops once the contour reaches a sharp edge. There will have to be more written about this after some testing. (To reproduce results you obtained with the older versions of Pixcavator just keep this value at 0.)

UGss-sliders.jpg

A new header is Data filtering. There are only two buttons here currently – Unmark dark and Unmark light. For convenience they were redesigned as follows. These are toggle buttons so that you can choose to concentrate on only, say, light objects without having to unmark dark every time you change the settings. There is more to come here.

The analysis summary now includes the mean values and standard deviations of all the main characteristics of objects (marked only).

The way contours are plotted was improved. Now red and green contours never overlap no matter how close they are to each other.

A noticeable speed-up was achieved, in both image analysis and graph analysis part. The memory usage was significantly reduced. There were also numerous minor improvements.

3.4 Version 3.0

July 6, 2008

RGB channel-by-channel analysis. It’s an experimental feature, so that you can only use the red or the green for now. This is important for some applications such as microscopy. Different features are sometimes better revealed in different channels. Below: original, analysis in red channel, analysis in green channel.

Epithelial-cells.jpg Epithelial-cells 2044 89RED.jpg Epithelial-cells 1967 36GREEN.jpg

Analysis summary to include some statistics. The output table contains only the raw data about each object. Of course, if you save the data to Excel, you can get anything from it: average of all columns, histograms, etc. We thought that it would be nice to be able to preview some data: average values of size and contrast. There will be more.

Data-under.jpg
Seeds 99 53.jpg

Data displayed based on the location of the mouse. That’s another very convenient feature. You used to have to mark/unmark object in the image and then find the row in the table to see the objects' measurements. That’s not fun if the table is a hundred rows long. Now you let the mouse hover over the object of your interest and the data from the table is displayed right beneath the image.

Coloring objects. This feature is coloring objects.

Hiding contours. To see the original image you used to have to go to the Analysis tab. Now you can flick it on and off to see what is hiding under the contours. The marking/unmarking of objects is unaffected.

Some sliders removed. The sliders for roundness and saliency haven’t been used a lot as far as I know. The complexity they add did not seem worthwhile. It does not mean that there will be always just the two sliders. The development of new characteristics for the sliders is under way. They will only be added if they make a significant improvement over what we have now. At least one new slider is coming in the next release.

Shrink slider modified. The shrink slider used to give you the shrink factor in terms of the area of the image. Now if you set it at 2, both of the dimensions will be cut in half while the area (and the processing time) will be cut by 4. This seems simpler. It is also preset to cut the processing time to 10 seconds or less. It seems like 99% of the time the resolution is excessive relative to the features being sought.

3.5 Version 2.4

February 1, 2008

These are the changes in comparison to version 2.3:

  • The interface has been streamlined. Pushing “Run” will now take you straight to the output. The “simplification” sliders have been removed (they will reappear in the image editing version of Pixcavator to appear in the near future).
  • More data is provided about the objects in the image. The table now contains additionally: roundness, perimeter, and average contrast.
  • Some bugs have been fixed. In particular, computation of the contrast and the saliency for light objects was incorrect. The computation of perimeter and roundness has been made more accurate (see the discussion Lengths of curves).

4 2007

4.1 Version 2.3

July 18, 2007

The main new feature is that Pixcavator will display contours of objects not just squares as before. The difference is enormous! And now you can also select objects by clicking on them. Then you can remove them one by one or save them as a separate image. We have also added a collection of standard image processing tools.

4.2 Versions 2.2.1 and 2.2.2

March 25, 2007

A couple of bugs are fixed and many cosmetic modifications have been made. Also, you can now use the “Cancel” button to stop processing. On another level, the way the sizes of objects is computed is corrected.


4.3 Version 2.2

February 17, 2007

Several new features have been added and the interface has been completely redesigned. There are now three tabs:

  • Analysis. As before the original image and the simplification settings are displayed. After the analysis is run, the simplified image is also displayed.
  • Tools. It contains a few image processing tools: brightness and contrast adjustment, dilation, erosion, histogram equalization, etc.
  • Output. Here the output data is displayed. First, the output includes the list of objects in the image along with their locations and measurements. Secondly, the image is displayed with the objects captured by squares. When an object on the list is marked and unmarked, the corresponding square appears and disappears. The sliders of the simplification settings are also displayed. As these sliders are moved, the table and the squares are instantly updated.

The new version can run in all resolutions from 800×600 and higher.

4.4 Version 2.1

January 19, 2007

A couple of bugs have been fixed and a disabled slider has been enabled.


4.5 Version 2.0

January 15, 2007

There are still a couple of bugs and rough edges but this is a completely different level. Objects are listed in a table and squares are placed over them in the image. It is slower, so for the simplification tasks use version 1.9.

5 2006

5.1 Version 1.9

November 29, 2006

Not quite version 2 yet... Changes in the new version:

  • A new simplification setting has been added, saliency. It’s the volume of the object, if you know what I mean…
  • Color images are analyzed as well now. Separately for each of the three colors, sorry.
  • “Advanced processing” includes pre- and post-processing options, the gray scale analysis option, and several custom simplification settings as double sliders. These can be made use of with…

Pixcavator SDK finally arrives. You can edit the code for the GUI, pre- and post-processing, simplification settings as combinations of integrals, etc. Version 2.0 will provide the full output – a list of all objects with their areas, locations, and other data. Even with version 1.9, a lot of work lies ahead – most of the options are still missing, documentation is rudimentary, etc…

5.2 Version 1.2

October 14, 2006

  • The interface has been reworked. Windows and buttons are rearranged, so that the images can be larger.
  • Graphics has been changed.
  • A new simplification parameter has been added – compactness or roundness. It is computed as (perimeter squared)/(4*PI*area). As before if the compactness of an objects is less than this setting, the object is removed from the image. There is also an unused setting. Conceivably, the user can introduce something of his own.
  • The memory leakage problem has been solved.
  • For your convenience, the option of shrinking the image prior to processing has been added. Two bugs have been fixed.
  • There is still a bug.

5.3 Version 1.1

September 11, 2006

  • This is now a single file distribution (one still needs GDIPLUS.DLL on machines with Win2K and Win98),
  • Memory usage has been reduced significantly,
  • I've removed histogram stretching. Frequently, the processed image used to be darker than the original. Now it may be lighter. We’ll see if it’s better…
  • A couple of small bugs fixed.

5.4 Version 1.0

September 5, 2006

Pixcavator.zip (3.87 MB). Right click to save to a folder, then extract the files from the zip-file (either double click on it or right click and choose Extract), then run Pixcavator.exe. Only for Windows XP…