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MorphEm

CaicedoLab

MorphEm is a self supervised learning framework trained with the DINO Bag of Channels recipe on the entire CHAMMI-75 dataset. It serves as a benchmark for performance for self-supervised models. The model was pre-trained with a heterogenous dataset of microscopy images with the goal of obtaining cell morphology embeddings for biological applications. The primary use of this model is feature extraction of cellular morphology in image-based biological experiments. The model takes single-channel images as input and produces feature vectors with discriminative information of cellular phenotypes. The input images should be segmented ahead of time; this model does not identify the location of cells automatically. The feature embeddings have been tested in single-cell analysis problems. If the images of interest are multi-channel, each channel can be processed independently and then the feature embeddings of all channels are concatenated for downstream applications. The applications of the embeddings produced by this model include basic biology research, functional genomics studies, drug discovery projects, among others.

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MorphEm

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