Abstract
Electron microscopy (EM) enables high-resolution visualization of protein distributions in biological tissues. For detection, gold nanoparticles are typically used as an electron-dense marker for immunohistochemically labeled proteins. Manual annotation of gold particle labels is laborious and time consuming, as gold particle counts can exceed 100,000 across hundreds of image segments to obtain conclusive data sets. To automate this process, we developed Gold Digger, a software tool that uses a modified pix2pix deep learning network capable of detecting and annotating colloidal gold particles in biological EM images obtained from both freeze-fracture replicas and plastic sections prepared with the post-embedding method. Gold Digger performs at near-human-level accuracy, can handle large images, and includes a user-friendly tool with a graphical interface for proof reading outputs by users. Manual error correction also helps for continued re-training of the network to improve annotation accuracy over time. Gold Digger thus enables rapid high-throughput analysis of immunogold-labeled EM data and is freely available to the research community.
Highlights
Electron microscopy (EM) enables high-resolution visualization of protein distributions in biological tissues
The annotated images are fed to the discriminator network, which is tasked with discerning between the outcome image created by the generator (“fake”), and the ground truth created by a human expert (“real”) (Fig. 1d)
We present our Gold Digger software for annotating colloidal gold particles in EM images
Summary
Electron microscopy (EM) enables high-resolution visualization of protein distributions in biological tissues. Manual annotation of gold particle labels is laborious and time consuming, as gold particle counts can exceed 100,000 across hundreds of image segments to obtain conclusive data sets To automate this process, we developed Gold Digger, a software tool that uses a modified pix2pix deep learning network capable of detecting and annotating colloidal gold particles in biological EM images obtained from both freeze-fracture replicas and plastic sections prepared with the post-embedding method. EM immunolabeling techniques that use colloidal gold particles include both post-embedding approaches as well as the freeze-fracture replica immunogold labeling (FRIL) method The latter provides for exacting quantification of membrane protein distributions with high specificity and e fficacy[1,2]. Gold Digger’s applicability on completely novel image sets, along with its generalizability, is a significant improvement relative to other solutions for gold particle identification in FRIL images
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