It is typically realized in a line or a tile by tile scanning fashion in order to allow the imaging and visualization of samples exceeding the field of view of a conventional light microscope setup. Whole slide imaging (WSI) is the process of acquiring images of tissue sections. Thus, relevant data can be combined and analyzed throughout all registered slides, facilitating the analysis of correlative results for multiplexed and multimodal imaging. In addition, the transformations can be applied in QuPath to produce on-the-fly transformed images that can be displayed on top of the reference image. These transformations can then be retrieved in QuPath to transfer any regions of interest from an image to the corresponding registered images. Each registration is automated by using an elastix backend, or semi-automated by using BigWarp in order to interactively correct the results of the automated registration. Fiji is then used to open the QuPath project and perform the registrations. The set of whole slide images to register and analyze is at first defined as a QuPath project. Using pre-existing software components and developing missing ones, we propose a user-friendly workflow which facilitates the nonlinear registration of whole slide images in order to reach sub-cellular resolution level. In both cases slight deformations from one image to another are unavoidable, leading to an imperfect superimposition Redundant and thus a loss of accuracy making it difficult to link measurements, in particular at the cellular level. Indeed, for multiplexing, as well as multimodal imaging, it is indispensable that the same sample is imaged multiple times, either through various systems for multimodal imaging, or using the same system but throughout rounds of sample manipulation (e.g. Image analysis workflows for Histology increasingly require the correlation and combination of measurements across several whole slide images. 3Histology Core Facility, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.2Imaging Consulting, Altlussheim, Germany.1Bioimaging and Optics Core Facility, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.I am so confused, so I really appreciate any help from you.Nicolas Chiaruttini 1* Olivier Burri 1 Peter Haub 2 Romain Guiet 1 Jessica Sordet-Dessimoz 3 Arne Seitz 1* Do I need to care about the Mean fluorescence of background?.Is the red or green fluorescence intensity affected by area/size of oocytes? In case I have several oocytes in one image (some oocytes are smaller than others), and I want to calculate the red or green fluorescence intensity for each oocyte, do I need to choose an identical area for oocytes? And after having fluorescence intensity for each oocyte, can I calculate the mean of red or green fluorescence intensities from it?.After that, a result table appeared, and the red or green fluorescence intensity was “Integrated intensity”. And then chose “Analyze -> Measure” to calculate red or green fluorescence intensity.Then set functions: Analyze -> Set Measurements -> chose “Area, SD, Min and Max gray value, Integrated intensity, Mean gray value”.In each red or green fluorescence image, they chose 1 oocyte to be ROI. I saw the pictures of staining oocytes which show 2 colours (red and green), but I am not sure how they quantify the red and green fluorescence intensity from these pictures. I am learning how to use Image J to calculate fluorescence intensity.
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