Qupath fluorescence. Multichannel fluorescence & multiple classifications

Discussion in 'add' started by Nikolabar , Wednesday, February 23, 2022 12:12:30 PM.

  1. Vular

    Vular

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    Detection and classification of cells. The ability to switch visualizations helps to discern what exactly this means. However, this will require additional computational time and human input to perform. When using automated approaches for cell detection and quantification it is prudent to optimize the automated cell detection parameters for each individual project because of differences in staining protocols, image acquisition and regional differences in staining intensity in subregions of a tissue sample Roeder et al. In our tissue however, a visual inspection of the rare dual-classified DsRed and GFP-positive cells revealed these were individual DsRed and GFP-positive cells with nuclei that were in close proximity Fig. Analysis of fluorescence images.
     
  2. Tugrel

    Tugrel

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    Detect & measure cells¶. QuPath's default Cell detection command can be applied for fluorescence and multiplexed images, not only brightfield. The key.Extended Data Figure Example of optimization annotations.
     
  3. Tuhn

    Tuhn

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    In the easier case of fluorescence images, QuPath assumes that each channel of the image corresponds to a different stain or marker of some kind.In our study we did not expect DsRed and GFP to colocalize as NG2 and CX 3 CR1, considered markers of pericytes and microglia in the brain, respectively, have not, to the best of our knowledge, been reported to colocalize in the same cells in the healthy adult brain.
     
  4. Mudal

    Mudal

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    QuPath's Cell detection command can be applied to both brightfield and fluorescence images. The key thing is that the Image type needs to be set.Adding fails with a message that is only reported in the log.
     
  5. Sashakar

    Sashakar

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    I am trying to analyze fluorescent images taken on delta vision systems. I am staining for 3 surface markers and DAPI stain.The cortex had a significantly higher proportion of GFP-positive microglia 5.
     
  6. Kazibei

    Kazibei

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    cumperi.online › qupath-users.An alternative is to replace the mean with the medianand the standard deviation with the median absolute deviation MAD.
     
  7. Zolomuro

    Zolomuro

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    Hello, recently I started working with QuPath and analyzing light microscopic tissue images is quite impressing in terms of segmentation and classification.Outside QuPath or in the Script editor create a list of the channel names you want, with a separate line for each name.
     
  8. Grorisar

    Grorisar

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    In QuPath, fluorescent cell detection can be performed using any channel but most commonly utilises a nuclear stain such as DAPI to first detect.Download FigureTIF file.
    Qupath fluorescence.
     
  9. Fejind

    Fejind

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    petebankhead added a commit to petebankhead/qupath that referenced Fixed bug when calculating intensity features for RGB fluorescence.QuPath also has the capability to analyze tissue labeled with fluorescent markers, a feature which offers a number of advantages including higher dynamic range and easier multiplexing, leading to better identification of colocalized targets and allowing the user the ability to determine spatial relationships between different cell types.Forum Qupath fluorescence
     
  10. Dagul

    Dagul

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    Set type of image to Fluorescence. Designating the grayscale image as fluorescent tells QuPath cell. (object) detection to look for light objects on a dark.The files generated by slide scanning microscopes are large and difficult to handle for many common image analysis programs, including open-source software such as ImageJ and CellProfiler.
     
  11. Gardatilar

    Gardatilar

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    Labels bug.
     
  12. Mazurisar

    Mazurisar

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    Below we discuss the importance of optimizing the QuPath cell detection parameters for each project.
     
  13. Gakus

    Gakus

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    Please read Part 2 for more details.
    Qupath fluorescence.
     
  14. Nerisar

    Nerisar

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    Here, we provide the first investigation utilizing QuPath to detect multiple types of fluorescently-labeled cells in mouse brain tissue sections, specifically pericytes expressing DsRed and microglia expressing GFP.
     
  15. Daramar

    Daramar

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    Ideally, the stain vectors should tightly surround the majority of the scattered points.
    Qupath fluorescence.
     
  16. Kinos

    Kinos

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    forum? Bug report Describe the bug Add intensity measurements fails with error below when run on a JPG image set to image type fluorescence.
     
  17. Mizshura

    Mizshura

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    forum? I can check roughly the intensity values in the DAPI channel inside and outside nuclei by moving my mouse over the image, and cross-referencing the pixel values displayed on the bottom right of the viewer.
     
  18. Aranris

    Aranris

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    QuPath users.
     
  19. Barisar

    Barisar

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    QuPath does not hold the actual image files but rather links to the original images, and so it was ensured that the project file and original image files were never separated.
     
  20. Dousar

    Dousar

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    Whatever the cause, the finding that different subregions of interest required different cell detection parameters highlights the importance of optimizing detection parameters in each experiment, especially when attempting to compare cell numbers from region to region.
     
  21. Zolonris

    Zolonris

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    Please read Part 2 for more details.
     
  22. Zuluzshura

    Zuluzshura

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    Cells having measurements with values greater than or equal to the threshold will be assigned the classification selected through the Above threshold drop-down list, and the rest assigned the classification through Below threshold.
     
  23. Zulumi

    Zulumi

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    QuPath can integrate with ImageJ and other packages to reuse carefully developed analysis tools and allows the user to rapidly analyze high resolution images without requiring expensive, specialized computing facilities and without having to rely on sampling smaller regions of interest.Forum Qupath fluorescence
     
  24. Shaktishicage

    Shaktishicage

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    forum? The precise percentage of cells that are microglia in mouse brains has rarely been quantified.
     
  25. Kazrajas

    Kazrajas

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    This is the first of a two-part series looking at how QuPath can handle multiple classifications to start working more meaningfully with multiplex images.
     
  26. Kazigar

    Kazigar

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    After setting the channel, I click Run and… nothing is detected.
     

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