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= Annotated Image
|Subject||Mus musculus, E16.5|
Labeled Proteins: Sox9
Marker for: chondrocyte, epithelial cell, unclassified fibroblast, pre-alveolar epithelial cell
Labeled Proteins: Sftpc
Marker for: intermediate pneumocyte, type II pneumocyte precursor cell
|Notes||This image displays both manual (done by a person) and computer generated ("machine") annotations. Choose the "Features" tab above to work with the annotations.
Machine annotation is a process of automated segmentation based on machine learning that uses an algorithm to outline structures. A challenge with this process is the small number of images for a probe set and developmental stage, hence we need optimal conditions and context-based constraints to guide the machine learning. We developed code libraries to optimize images by correcting for spatial bias in intensity, differential staining across images, and separation of colors into bands to correspond to standard fluorescent probes. Our code libraries apply an ontology to constrain the type of structures targeted by a given antibody probe set, and the cells/tissues identifiable within each structure, limiting the number of classification classes and increasing the probable accuracy of the displayed results.
Annotations can be turned off and on by toggling the checkboxes below.
Fluorescently-labeled secondary antibodies are used to visualize protein localization. Confocal images are pseudo-colored with different colors to represent different proteins in the image. When more than one protein is present in close approximation to each other, the colors will blend into a different color than the original pseudo-colored protein. For example, when red and green are merged, the color will be yellow if the two proteins are in close approximation. If the proteins are at different concentrations or are slightly further away from each other the color will be orange. If the proteins are not within a defined approximation range from each other (depending on magnification) their original colors will appear. The color wheel is provided to helps visualize the merged colors in the fluorescent image.