Large file with large number of objects
Good morning,
I have very large files ~1GB and I want to quantify about 1000 red objects. I am collecting Area, Percent Area, and integrated OD. Usually it takes a long time, or crashes when I press count. So I made a range, and now when I collect the data, it puts it into 2 classes. However, when I try this on other images it does not work, or it changes the selection of objects after manual segmentation. Also, when I try to classify the blue objects, I choose a range, and it crashes even though it put the red ones into 2 classes. I was wondering since I do not need to count the number of objects, (I just need area, percent area, and integrated OD), what is the best way to go about this?
I have very large files ~1GB and I want to quantify about 1000 red objects. I am collecting Area, Percent Area, and integrated OD. Usually it takes a long time, or crashes when I press count. So I made a range, and now when I collect the data, it puts it into 2 classes. However, when I try this on other images it does not work, or it changes the selection of objects after manual segmentation. Also, when I try to classify the blue objects, I choose a range, and it crashes even though it put the red ones into 2 classes. I was wondering since I do not need to count the number of objects, (I just need area, percent area, and integrated OD), what is the best way to go about this?
0
Answers
coco18c --
What is the average DIMENSION (W x H x BIT DEPTH) of your IMAGE (in PIXELS)?
What is the average DIMENSION (W x H or DIAMETER) of the RED OBJECTS and the BLUE OBJECTS (in PIXELS)?
I think having this information will be helpful to us trying to assist you.
Thanks.
-- Matt
Right click on an IMAGE within PREMIER and select the I ICON for DOCUMENT PROPERTIES
The dialog box that will be displayed will provide the information within the EXPERT TEMPLATE under SIZE and INTERPRETATION.
-- Matt
Premier can handle 1000 objects without problems, another issue is that your image size can be too big for the RAM. Are you counting 1GB file at full resolution? The segmentation and measurements create additional buffers, so they may require several times more RAM than the image size, so you should be sure that you have enough RAM.
I can suggest some options to try:
1. If your objects bigger than several pixels in diameter, you may try to resize image before Count.
2. If you need full resolution, you may use floating ROI and count objects in ROIs collecting the full image data in the Data Collector.
If none of these solutions work for you and you think you have enough RAM, then please send us the image and the measurement options file you use (IQO).
BTW, are you using Threshold segmentation or Smart segmentation? Smart segmentation may require much more RAM then threshold segmentation, depending on the number of channels in the recipe.
Yuri
Also, this is the number of pixels for the image:
So, I usually open up the file and then use manual segmentation using the threshold tool.
I want to be able to count the Area, percent area, and integrated OD for both the blue and red objects.
It usually crashes, like the image below and stops at 60% even with ROI.
So I tried using a smaller ROI, and works, but I was wondering how do I make multiple ROI without overlapping? For example, can I make a grid of ROI, turn all but one off, and then count? And repeat this process? I'm not sure if that is the best method. But I am looking for ideas!
It looks like your may run out of RAM counting the large 1.4GB image when you have only 12GB of RAM. One way to avoid the problem is to resize the image (50%, or 25%). If you need area percentage and optical density resizing the image should not affect the measurement results.
Also, try to reduce the list of measurements only to the necessary, so RAM is not used unnecessary. You can also extract only one channel from your 24-bit RGB image, e.g. Green (complimentary for Red) and do measurements on that image, it will make the image size in RAM 3 times smaller. (8 bits instead of 24)
There are several way to do measurements per object.
1. Create ROI of one object, Count, collect data to Data Collector. Clear ROIs and draw ROI around another object and repeat the steps.
2. or Draw Measurement outlines using Class1 around every parent feature. Activate "Preserve existing features", "Use as Outlines" in the measurement options and Count red objects.
Be sure that the Parent measurement is active, then in the measurement table activate Group by Parent, so you get statistics for any measurement per parent object:
Yuri
Regarding the last question: you can define the measurements you need in the Types dialog (Count/Size tab), there you can choose area, percent area, and integrated OD...
You may also check some video tutorials to see how to do measurements in Premier: http://www.mediacy.com/resources/media
If you still have the problem, save the measurement options file (IQO) and upload it together with the image to this link: Click here to upload files.
Yuri