Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images.
Per SVK's suggestion, it is worth exploring if one can use an autoencoder (regular or variational) instead of PCA for the sliding-window-based image denoising originally written by @ramav87 .
Is your feature request related to a problem? Please describe.
In current version it is not possible to get just cell detection and cell analysis without cell classification. This could be potentially beneficial if you are analyzing cFos (nuclear) staining. With parameters that can be changed in cellfinder now I was able to get very good cFos detection results. When classification is done mor
The semantic segmentation models need to be extended to work with 3D data. This should be very straightforward - just introduce an option to select between 1D, 2D, and 3D cases to ConvBlock, [UpsampleBlock](https://g
Currently, the routes of tracingstore and datastore require the token as GET parameter. They should also read it from the header if present. This was already implemented for the zarr routes in #6144
Installing brainreg brings in 3.4GB of dependencies, as measured by my virtualenv folder's size. I see many things I don't think(?!) I need for a simple registration - e.g. ipython, jinja2, pyside2, sphinx, and napari. [I could be wrong here, of course.]
Might I suggest verifying what is needed, and perhaps having separate extras for some of this functionality? This could leave the core "pip
This is the official implementation of our publication "Deep learning enables fast and dense single-molecule localization with high accuracy" (Nature Methods)
ImSwitch is a software solution in Python that aims at generalizing microscope control by providing a solution for flexible control of multiple microscope modalities.
Per SVK's suggestion, it is worth exploring if one can use an autoencoder (regular or variational) instead of PCA for the sliding-window-based image denoising originally written by @ramav87 .
@saimani5 @markpoxley will you be interested in exploring it?