Mithunjack / Thesis-NeRFs

Denoising 3D TEM tomography via Advanced Neural Radiance Fields(NeRF)
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Thesis Title: Denoising 3D TEM tomography via Advanced Neural Radiance Fields(NeRF)

Thesis Presentation Slides 💥

Architecture 🧩

Thesis Architecture

Result Denoising

TEM Dataset 1

TEM Dataset 2

TEM Dataset 3

TEM Dataset 4

STEM Dataset 1

STEM Dataset 2

Synthetic Dataset

3D Construction of TEM image(Dataset 4)

TEM_Data_img

Usefull tools for Literature Review 🛠️

Click to expand! 1. It provides an overview of any article and all related research with the assistance of AI -> [Paper Digest](https://www.paperdigest.org/review/). 2. The AI Research Assistant -> [Elicit](https://elicit.org/) | [Scispace](https://typeset.io/) 3. An app that visualizes all of the related papers for a specific paper -> [Litmap](https://www.litmaps.com/) 4. Similar to Litmap, but using a different linked paper visualization website-> [Connected paper](https://www.connectedpapers.com/) 5. For improved writing efficiency -> [Writefull](https://www.writefull.com/) 6. For creating custom vectors or biologically themed graphics -> [Bio render](https://biorender.com/) 7. Similarly, litmap and connected paper provide another option -> [scite](https://scite.ai/) 8. Reference Manager -> [Zotero](https://www.zotero.org/) 9. Alternative Reference Manager -> [Mandele](https://www.mendeley.com/?interaction_required=true)

Useful Commands 👽

Click to expand! ## Linux 🤸 1. CUDA Version `nvidia-smi` // 11.8 2. Python Version `python3 --version` // 3.8.15 3. Clear cmd `reset` 4. Conda path setup [path](https://askubuntu.com/questions/849470/how-do-i-activate-a-conda-environment-in-my-bashrc) 5. Ubuntu architecture `uname -m` // x86_64 6. Ubuntu version and machine id `hostnamectl` 7. NVCC version `nvcc -V` 8. To find or locate file `locate {nvcc}` 9. PyTorch version `pip3 show torch` // 1.12.1+cu113 10. Linux background processing `htop` 11. Kill VS Code server `Remote-SSH: kill VS Code Server on Host` [Documentation](https://github.com/microsoft/vscode-remote-release/issues/4307) 12. Installing stuff without `sudo` [Documentation](https://askubuntu.com/questions/339/how-can-i-install-a-package-without-root-access) 13. Extract file `tar -xvf cmake-3.x.x.tar.gz` 14. Debian-based Linux Distribution: `cat /etc/os-release` 15. Change GPU `export CUDA_VISIBLE_DEVICES=1` 16. For building CMAKE `cmake . -B build -DCMAKE_CUDA_COMPILER:STRING="/usr/local/cuda-11.8/bin/nvcc"` #### [NeRFstudio Documentation](https://docs.nerf.studio/en/latest/quickstart/installation.html) 📄 **NerfStudio ✈️** 1. Check available model `ns-train --help` 2. Torch version check in Anaconda `pip3 show torch` 3. With a specified websocket port `ns-train nerfacto --vis viewer --viewer.websocket-port=7008` 4. Resume training from one certain point `ns-train nerfacto --data data/nerfstudio/poster --trainer.load-dir {outputs/.../nerfstudio_models}` 5. Pre processing custom data `ns-process-data images --data data/custom_data --output-dir outputs/custom_data_preprocessed --no-gpu` **Anaconda 🐍** 1. Creating conda env `conda create --name nerfstudio -y python=3.8` 2. Activate env `conda activate nerfstudio` 3. Active env `conda info -e` 4. Jupyter notebook password [setup](https://jupyter-notebook.readthedocs.io/en/stable/public_server.html) 5. Remove env `conda env remove -n ENV_NAME` 6. Remove all env `conda remove --name myenv --all` 7. Env list `conda env list`