What I am using now is Binary Feature Extractor function in BioVoxxel plugin. Thus, some another solution must be applied. Unfortunately this “supporting” staining was not supportive enough i.e. Of course I wouldn’t like to draw the cells’ borders manually in hundreds of pictures and I hoped that some edge detection tool would do it for me. My first idea was that I could use some edge detection tool to obtain a map of the cells’ borders based on this staining and then somehow overlap it with a map of my protein of interest expression and use this to count positive and negative cells. There is also staining of yet another protein which locates in cell membrane which I hoped would be useful to delineate cells’ borders for the analysis. I have wide-field images of immunostained cells with nuclei stained with DAPI and my protein of interest stained with another fluorophore. Expression of the protein is scattered all over the cell with no regular pattern with some tendency to be in a proximity of nucleus. Maybe someone more familiar with image analysis can help me with this. I am using ImageJ to solve this problem but I believe that there is better solution than the one that I came up with. Of course I would like the computer to do it for me. I would like to quantify the fraction of both depending on certain culture conditions. Some of them do express it, some others don’t. Medical Laboratory Technology, Health Informatics, General Pharmacology, Toxicology and Pharmaceutics, General Immunology and Microbiology, General Biochemistry, Genetics and Molecular Biology, General Neuroscience National CategoryĮngineering and Technology Research subject Bioinformatics Bioinformatics Computerized Image Processing Identifiers URN: urn:nbn:se:uu:diva-458303 DOI: 10.1002/cpz1.89 PubMedID: 34038030 OAI: oai:DiVA.My protein of interest is not equally expressed among the cells in culture. ImageJ and CellProfiler are both committed to interoperability between their platforms, with ongoing development to improve how both are leveraged from the other Place, publisher, year, edition, pagesJohn Wiley & Sons, 2021. While both programs can be and are often used separately, these pipelines demonstrate the benefits of using them together for image analysis workflows. No single platform can provide all the key and most efficient functionality needed for all studies. Here, we share two pipelines demonstrating mechanisms for productively and conveniently integrating ImageJ and CellProfiler for (1) studying cell morphology and migration via tracking, and (2) advanced stitching techniques for handling large, tiled image sets to improve segmentation. ![]() Although many image analysis problems can be well solved with one or the other, using these two platforms together in a single workflow can be powerful. ImageJ's traditional strength is in single-image processing and investigation, while CellProfiler is designed for building large-scale, modular analysis pipelines. ImageJ and CellProfiler have long been leading open-source platforms in the field of bioimage analysis. 1, no 5 Article in journal (Refereed) Published Abstract ![]() Show others and affiliations 2021 (English) In: Current Protocols in Microbiology, ISSN 1934-8525, E-ISSN 1088-7423, Vol.
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