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Pytorch 3D Integrated Cell

Model Architecture

Building a 3D Integrated Cell: https://www.biorxiv.org/content/early/2017/12/21/238378

For the 2D manuscript and software:

Generative Modeling with Conditional Autoencoders: Building an Integrated Cell
Manuscript: https://arxiv.org/abs/1705.00092
GitHub: https://github.com/AllenCellModeling/torch_integrated_cell

Todo Items

  • GIT

    • Remove old big files from git

  • Jupyter notebooks

    • Check-in current state to git
    • Make sure notebooks all run and can produce figures
    • Annotate notebooks (notebook purpose)
    • Clear outputs
    • Check-in final state to git

  • Data

    • Make sure current Quilt data works
    • Check-in manuscript data to Quilt

  • Code

    • Check-in current state to git
    • Clear unused code
    • Clean up and annotate main functions
    • Check-in final state to git

  • Demos/Docs

    • Installation instructions
    • Getting Started doc
    • Demos for different training methods
    • Update doc figures

Support

This code is in active development and is used within our organization. We are currently not supporting this code for external use and are simply releasing the code to the community AS IS. The community is welcome to submit issues, but you should not expect an active response.

System requirements

We recommend installation on Linux and an NVIDIA graphics card with 10+ GB of RAM (e.g., NVIDIA Titan X Pascal) with the latest drivers installed.

Installation

Installing on linux is recommended.

  • Install Python 3.6+/Docker/etc if necessary.
  • All commands listed below assume the bash shell.

Installation method (A): In Existing Workspace

(Optional) Make a fresh conda repo. (This will mess up some libraries if inside a some of Nvidia's Docker images)

conda create --name pytorch_integrated_cell python=3.7
conda activate pytorch_integrated_cell

Clone and install the repo

git clone https://github.com/AllenCellModeling/pytorch_integrated_cell
cd pytorch_integrated_cell
pip install -e .

If you want to do some development, install the pre-commit hooks:

pip install pre-commit
pre-commit install

(Optional) Clone and install Nvidia Apex for half-precision computation Please follow the instructions on the Nvidia Apex github page: https://github.com/NVIDIA/apex

Installation method (B): Docker

We build on Nvidia Docker images. In our tests this runs very slightly slower than (A) although your mileage may vary. This comes with Nvidia Apex.

git clone https://github.com/AllenCellModeling/pytorch_integrated_cell
cd pytorch_integrated_cell
docker build -t aics/pytorch_integrated_cell -f Dockerfile .

Data

Data can be downloaded via Quilt T3. The following script will dump the complete 2D and 3D dataset into ./data/. This may take a long time depending on your connection.

python download_data.py

The dataset is about 250gb.

Training Models

Models are trained by via command line argument. A typical training call looks something like:

ic_train_model \
        --gpu_ids 0 \
        --model_type ae \
        --save_parent ./ \
        --lr_enc 2E-4 --lr_dec 2E-4 \
        --data_save_path ./data.pyt \
		--imdir ./data/ \
        --crit_recon integrated_cell.losses.BatchMSELoss \
        --kwargs_crit_recon '{}' \
        --network_name vaegan2D_cgan \
        --kwargs_enc '{"n_classes": 24, "ch_ref": [0, 2], "ch_target": [1], "n_channels": 2, "n_channels_target": 1, "n_latent_dim": 512, "n_ref": 512}'  \
        --kwargs_enc_optim '{"betas": [0.9, 0.999]}' \
        --kwargs_dec '{"n_classes": 24, "n_channels": 2, "n_channels_target": 1, "ch_ref": [0, 2], "ch_target": [1], "n_latent_dim": 512, "n_ref": 512, "output_padding": [1,1], "activation_last": "softplus"}' \
        --kwargs_dec_optim '{"betas": [0.9, 0.999]}' \
        --kwargs_model '{"kld_reduction": "mean_batch", "objective": "H", "beta": 1E-2}' \
        --train_module cbvae2 \
        --dataProvider DataProvider \
        --kwargs_dp '{"crop_to": [160,96], "return2D": 1, "check_files": 0, "make_controls": 0, "csv_name": "controls/data_plus_controls.csv", "normalize_intensity": "avg_intensity"}' \
        --saveStateIter 1 --saveProgressIter 1 \
        --channels_pt1 0 1 2 \
        --batch_size 64  \
        --nepochs 300 \

This automatically creates a timestamped directory in the current directory ./.

For details on how to modify training options, please see the training documentation

Loading Modes

Models are loaded via python API. A typical loading call looks something like:

from integrated_cell import utils

model_dir = '/my_parent_directory/model_type/date_time/'
parent_dir = '/my_parent_directory/'

networks, data_provider, args = utils.load_network_from_dir(model_dir, parent_dir)

target_enc = networks['enc']
target_dec = networks['dec']

networks is a dictionary of the model subcomponents.
data_provider is the an object that contains train, validate, and test data.
args is a dictionary of the list of aguments passed to the model

For details on how to modify training options, please see the loading documentation

Project website

Example outputs of this model can be viewed at http://www.allencell.org.

Examples

Examples of how to run the code can be found in the 3D benchmarks section.

Citation

If you find this code useful in your research, please consider citing the following paper:

@article {Johnson238378,
author = {Johnson, Gregory R. and Donovan-Maiye, Rory M. and Maleckar, Mary M.},
title = {Building a 3D Integrated Cell},
year = {2017},
doi = {10.1101/238378},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2017/12/21/238378},
eprint = {https://www.biorxiv.org/content/early/2017/12/21/238378.full.pdf},
journal = {bioRxiv}
}

Contact

Gregory Johnson E-mail: gregj@alleninstitute.org

License

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.