{ "info": { "author": "Xiao Tan, Andrew Su, Quan Nguyen", "author_email": "xiao.tan@uq.edu.au, a.su@uq.net.au, quan.nguyen@imb.uq.edu.au", "bugtrack_url": null, "classifiers": [ "License :: OSI Approved :: MIT License", "Operating System :: OS Independent", "Programming Language :: Python :: 3" ], "description": "

\n\n\n## Introduction to SpaCell\n\n* **SpaCell** program has been developed for spatial transcriptomics dataset, which include image data and RNA expression data. \n\n* **SpaCell** implements (deep) neural network (NN) models like autoencoder, convolutional neural network (residual net), and pre-trained model for transfer-learning to train models for identifying cell types or predicting disease stages. The NN integrates millions of pixel intensity values with thousands of gene expression measurements from spatially-barcoded spots in a tissue.\n\n* **SpaCell** has a comprehensive data preprocessing workflow to filter, combine, and normalise images and gene expression matrices\n\n## Installation\n\n1. Requirements: \n\n```\n[python 3.6+]\n[TensorFlow 1.4.0]\n[scikit-learn 0.18]\n[keras 2.2.4]\n[staintools ]\n```\n2. Installation: \n\n2.1 Download from GitHub \n\n```git clone https://github.com/BiomedicalMachineLearning/Spacell.git```\n\n2.2 Install from PyPi \n\n```pip install SpaCell```\n\n## Usage\n\n### Configurations\n\n```config.py```\n\n1. Specify the dataset directory and output directory.\n2. Specify model parameters.\n\n### 1. Image Preprocessing\n\n```python image_normalization.py```\n\n### 2. Count Matrix PreProcessing\n\n```python count_matrix_normalization.py```\n\n### 3. Generate paired image and gene count training dataset\n\n```python dataset_management.py```\n\n### 4. Classification\n\n```python spacell_classification,py```\n\n### 5. Clustering\n\n```python spacell_clustering.py -i /path/to/one/image.jpg -l /path/to/iamge/tiles/ -c /path/to/count/matrix/ -e 100 -k 2 -o /path/to/output/```\n\n* `-e` is number of training epochs\n* `-k` is number of expected clusters\n\n## Results\n\n### Classification of ALS disease stages\n

\n \n \n\n ### Clustering for finding prostate cancer region\n\n

\n \n\n ### Clustering for finding inflamed stromal \n\n

\n \n\n\n## Dataset \nFor evaluating the algorithm, ALS (Amyotrophic lateral sclerosis) dataset and prostate cancer dataset can be used.\n\n## Citing Spacell \nIf you find Spacell useful in your research, please consider citing:\n\nXiao Tan, Andrew T Su, Quan Nguyen (2019). SpaCell: integrating tissue morphology and spatial gene expression to predict disease cells. (Manuscript is currently under-review)\n\n## The team\nThe software is under active development by the Biomedical Machine Learning group at Institute for Molecular Biology (IMB, University of Queensland). \n\nPlease contact Dr Quan Nguyen (quan.nguyen@uq.edu.au), Andrew Su (a.su@uq.edu.au), and Xiao Tan (xiao.tan@uq.edu.au) for issues, suggestion, and collaboration.\n\n\n\n", "description_content_type": "text/markdown", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/BiomedicalMachineLearning/Spacell.git", "keywords": "", "license": "", "maintainer": "", "maintainer_email": "", "name": "Spacell", "package_url": "https://pypi.org/project/Spacell/", "platform": "", "project_url": "https://pypi.org/project/Spacell/", "project_urls": { "Homepage": "https://github.com/BiomedicalMachineLearning/Spacell.git" }, "release_url": "https://pypi.org/project/Spacell/0.9.9/", "requires_dist": null, "requires_python": "", "summary": "Spacell Package", "version": "0.9.9" }, "last_serial": 5643228, "releases": { "0.0.1": [ { "comment_text": "", "digests": { "md5": "592f9295d279b475496588bf9dba6f80", "sha256": "01c242a12ae0cbca12be429916a20be6b646150b36ae35efc6ecd4d566e714a1" }, "downloads": -1, "filename": "SpaCell-0.0.1-py3-none-any.whl", "has_sig": false, "md5_digest": "592f9295d279b475496588bf9dba6f80", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 16500, "upload_time": "2019-08-05T23:36:34", "url": "https://files.pythonhosted.org/packages/a7/0c/401c3d9df16785e12e5213ee1b5ae6ccdf1ab972344d441b70d199b7aeec/SpaCell-0.0.1-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "c4a1a809e7089b4ad19a21e577f49d2d", "sha256": "d508c871511902a1e5cff83e096ccd1d4815047c47f7d741cd21eb3e5a96a3ed" }, "downloads": -1, "filename": "SpaCell-0.0.1.tar.gz", "has_sig": false, "md5_digest": "c4a1a809e7089b4ad19a21e577f49d2d", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 14043, "upload_time": "2019-08-05T23:36:36", "url": "https://files.pythonhosted.org/packages/49/d0/8c12bd0f031be6a90f157cf9374b44961be4bcd84f95d98eb9220dbed2f3/SpaCell-0.0.1.tar.gz" } ], "0.9.9": [ { "comment_text": "", "digests": { "md5": "0419c740a6ed421b987c02c3c3ecdb9f", "sha256": "435b8b779b936389d93759cf174c15888787a432d5c6bcde22fb57c22d11f71c" }, "downloads": -1, "filename": "Spacell-0.9.9-py3-none-any.whl", "has_sig": false, "md5_digest": "0419c740a6ed421b987c02c3c3ecdb9f", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 15958, "upload_time": "2019-08-07T05:43:45", "url": "https://files.pythonhosted.org/packages/9a/0f/08ed170268b86d6f10b6b03ef6a554391ce49461d465c8a7d0f99af66d76/Spacell-0.9.9-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "676fb48e061652d2ac6c0dc986a7aef1", "sha256": "b4703c81508f61c9ca21d27a3d1614083a4fbf8aa86973d1f4cd2fc013012467" }, "downloads": -1, "filename": "Spacell-0.9.9.tar.gz", "has_sig": false, "md5_digest": "676fb48e061652d2ac6c0dc986a7aef1", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 14596, "upload_time": "2019-08-07T05:43:47", "url": "https://files.pythonhosted.org/packages/e8/67/1b84c188fdc2e32d5c79d70396f4d1e480ff73a10d6bf527fb2b415c5e4e/Spacell-0.9.9.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "0419c740a6ed421b987c02c3c3ecdb9f", "sha256": "435b8b779b936389d93759cf174c15888787a432d5c6bcde22fb57c22d11f71c" }, "downloads": -1, "filename": "Spacell-0.9.9-py3-none-any.whl", "has_sig": false, "md5_digest": "0419c740a6ed421b987c02c3c3ecdb9f", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 15958, "upload_time": "2019-08-07T05:43:45", "url": "https://files.pythonhosted.org/packages/9a/0f/08ed170268b86d6f10b6b03ef6a554391ce49461d465c8a7d0f99af66d76/Spacell-0.9.9-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "676fb48e061652d2ac6c0dc986a7aef1", "sha256": "b4703c81508f61c9ca21d27a3d1614083a4fbf8aa86973d1f4cd2fc013012467" }, "downloads": -1, "filename": "Spacell-0.9.9.tar.gz", "has_sig": false, "md5_digest": "676fb48e061652d2ac6c0dc986a7aef1", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 14596, "upload_time": "2019-08-07T05:43:47", "url": "https://files.pythonhosted.org/packages/e8/67/1b84c188fdc2e32d5c79d70396f4d1e480ff73a10d6bf527fb2b415c5e4e/Spacell-0.9.9.tar.gz" } ] }