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Crashing after count, before data table collection

coco18ccoco18c
in Image-Pro General Discussions
Good morning, I have been experiencing crashing right after I hit count. It goes until 60% and crashes, with any size image. I'm not sure what to do.

Best Answer

  • YuriGYuriG
    Answer ✓
    What number of objects do you have (you can see it in the Count Results group of Count/Size tab)? And what number of measurements do you display in the data table (number of columns)?
    If you have very large number of objects and too many columns it will require much RAM and time.
    As I recommended earlier, you may set filter ranges for Area to filter out some small objects (generally noise), so the number of real objects to display will be manageable by the table and Excel.

    Yuri

Answers

  • YuriGYuriG
    It's hard to tell what the problem is without more details. You can try to reset options (File | Options | Reset button).
    Or send a sample image and measurement options file (ZIP them and attach to the forum post).

    Yuri

  • coco18ccoco18c
    Let me just explain what I am trying to use the program for. I am trying to quantify RBCs (dark red), neutrophils (blue), and infiltrated alveoli (white space) in lung images. I want to measure the area, intensity and optical density of the RBC and Neutrophils.  I have been able to select the RBCs and neutrophils with the manual selection tool, and have also selected the alveoli using this as well as the range tool. I also want to know how to calibrate the system using a lens. The manual says to use "predictive calibration," but I cannot see this on the dropdown bar. Also, I want to group by class name, and it will not let me do this; only "collapse" and "block" are options. I have also been experiencing a lot of crashing during batch processing (it won't load all of the pictures), data collection, making macros, and even opening the program itself.
    Attached is a zip file, it might have really bad resolution because I had to compress a lot, but you get the idea. My file sizes range from 600,000-1,000,000 KB




  • YuriGYuriG
    edited April 2017
    I checked the image and it looks normal. What I want to have is the measurement options file to see how you are doing segmentation. Can you please save the IQO file (from Measure tab) and attach to the forum?

    If you work with huge images (1GB or more) the memory handling issues become very important, so you should optimize your segmentation recipe to use minimal number of channels. How much RAM do you have in your PC?

    You can group by Class using the "Group by Class" menu item in the Grouping button drop-down of the measurement table.

    "Predictive calibration" can only be used if you have at least one lens calibrated. 

    Yuri

  • coco18ccoco18c
    The group by class drop down is not there. It used to be, but now it disappeared. So I'm not sure how to get it back again, but now there is a lot of data in the excel spread sheet. How do I calibrate by using the lens manufacturer, etc if I do not have predictive calibration?

    Processor: calculations per second: 7.4
    Memory: 7.7 (RAM)
    Graphics 6.8
    Primary hard disk 5.9


    It won't let me attach those files. But I just select all of the blue, and then all of the dark red and then press count. No ROIs.
  • YuriGYuriG
    You might be looking at different table (Data Collector?) be sure you look at Measurements data table.

    You can calibrate by some object of known length on the image (e.g. micrometer).

    How much RAM do you have (in GB)?

    You should ZIP the options file, then you can attach it.

    Yuri

  • coco18ccoco18c
    It's not showing up in the measurements data table. Is there any way I could call support? Do you have a telephone number?



  • YuriGYuriG
    You can send email to tech support techsupport@mediacy.com, though the entry cannot disappear by itself. Can you post a screenshot?
  • YuriGYuriG
    I checked your image with "Neutrophils, RBCs.rge" and it counts properly generating 2 classes. Though there are a lot of very small objects, I get 2854 object on that test image.



    If you don't need small objects (noise), you should set filter ranges to limit count only to objects of interest,  it will speed up the count and data collection/export.

    Yuri
  • coco18ccoco18c
    Hi,

    Attached are the screenshots. Let me know if you can help with the "group by class."
  • coco18ccoco18c
    Also, do you know how to "thin/skeletonize" this particular image. It doesn't come out very clear when I do it. I was wondering if you had any luck.
  • YuriGYuriG
    Your screenshots show Data Collector table (opened from Data Collector ribbon group), that's why it doesn't have "Group by Class" item. Measurements table can be opened from the View ribbon group on the Measure or Count/Size tabs, try that.

    Yuri
  • YuriGYuriG
    To skeletonize the image properly you must have correct binary image first (you may need to apply some filters to fill gaps or make image more contrast). Try creating binary mask first (using Mask button in the threshold dialog), then use Thinning filter in 2D or 3D filter panels.

    Yuri

  • coco18ccoco18c
    Ok so I tried clicking the "data table" button, but the program crashes and stops at 60% whenever I press this button. I have 12 GB of RAM. Would this be an issue?
  • coco18ccoco18c
    Ok that's probably it. It's about 300,000 objects. With three columns
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