{"repo":"PolarBean/DeepSlice","free":true,"listed":false,"github":"https://github.com/PolarBean/DeepSlice","clone":"git clone https://github.com/PolarBean/DeepSlice.git","description":"A python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning.","language":"Python","stars":127,"topics":["machine-learning","deep-learning","histology","histological-images","brain-imaging","automation","python","brainmap","brainmaps","neuroscience"],"license":"MIT","category":"machine-learning","readme_excerpt":"DeepSlice is a python library which automatically aligns mouse histology with the allen brain atlas common coordinate framework (and now rat brain histology to the Waxholm rat brain atlas, though this is in beta). The alignments are viewable, and refinable, using the QuickNII software package. DeepSlice requires no preprocessing and works on any stain, however we have found it performs best on brightfield images. At present one limitation is that it only works on Coronally cut sections, we will release an update in the future for sagittal and horizontally cut histology. DeepSlice automates the process of identifying exactly where in the brain a section lies, it can accomodate non-orthogonal cutting planes and will produce an image specific annotation for each section in your brain. Citation If you use DeepSlice in your work please cite Carey et al, 2023. It may also be useful if you mention the version you use :) In addition, you should also remember to cite Wang et al, 2020 if you use the Allen CCFv3 atlas for the Mouse model and Kleven et al, 2023 if you use the Waxholm Atlas of the Sprague Dawley Rat for the Rat model. Workflow DeepSlice is fully integrated with the QUINT workflow. Quint helps you register, segment and quantify brain wide datasets!   🐭🧠🔬💻🤖 Web Application If you would like to use DeepSlice but don't need your own personal installation, check out DeepSlice Flask , a web application which will allow you to upload your dataset and download the align","default_branch":null,"files":null,"tree":[],"storefront":"/r/PolarBean","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/PolarBean/DeepSlice/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}