Electron Microscopic Data Analysis
Project Readme
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Scope And Content | Instruction on how to run this project |
Scripts file (cdeep3m_py)
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Scope And Content | scripts for project |
Technical Details | caffe, python, keras with tensorflow backend |
Scripts file (MultiResUnet_scripts)
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Scope And Content | scripts for project |
Technical Details | caffe, python, keras with tensorflow backend |
Raw data
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Scope And Content | Training, Validation and Test data |
Technical Details | .png image files of size 1024x1024 |
Output data (DeepEM3D)
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Scope And Content | Output data |
Technical Details | contains intermediate output and final output |
Output data (MultiResUnet)
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Scope And Content | Output data |
Technical Details | contains intermediate output and final output |
- Collection
- Cite This Work
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Singhal, Tushar; Kolkur, Prashant; Ellisman, Mark H.; Altintas, Ilkay (2019). Electron Microscopic Data Analysis. In Data Science & Engineering Master of Advanced Study (DSE MAS) Capstone Projects. UC San Diego Library Digital Collections. https://doi.org/10.6075/J03N21QH
- Description
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Capstone Project for Data Science & Engineering Master's Program at UC Sand Diego (UCSD) 2019.
The “Electron Microscopic Data Analysis” project aims to support the processing, analysis and dissemination of large-scale 3D electron microscopic (EM) data derived from a remarkable collection of legacy biopsy brain samples from patients suffering from Alzheimer’s disease (AD). Alzheimer’s disease is a progressive neurodegenerative disease, leading to dementia accompanied by several structural changes in the brain of patients.
The project intends to facilitate the processing and downstream analysis of complete whole cell reconstructions of neurons from unique biopsy image samples of cerebral cortex taken from AD cases by Robert Terry in the 1960’s, focusing on early onset cases, where cells effected to differing extents are neighbored by cells without AD-associated forming paired helical filaments, (PHF) now known to be largely made up of tau proteins. These samples were screened and preliminarily reported on by Ellisman, Masliah and Terry (Ellisman et al., 1987) and manifest near perfect preservation of ultrastructure PHF and amyloid accumulations as well as modifications to subcellular organelles and cytoskeletons of the cell bodies, axonal and dendritic processes.
Raw data (or data) is coming from Cell Image Library (CIL: http://cellimagelibrary.org/cdeep3m). Cell Image library is a public and easily accessible resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes. The purpose of this database is to advance research on cellular activity, with the ultimate goal of improving human health. This data is accessed manually from the website and copied to the memory disk for processing. The data is a serial block face scanning electron microscopy (SBEM) 3D data volumes. Serial block-face scanning electron microscopy (SBEM) is a way to obtain high resolution 3D images from a sample. This method is particularly good at imaging large fields-of-view in X,Y,Z that is 3dimension at nanometer resolution. The data is brain image samples of patients suffering from Alzheimer’s disease. The Alzheimer's image data images are of very high definition. The size of a typical image in multiple datasets is in the range of 16000x10000x400 pixels images. - Creation Date
- 2019-01 to 2019-06
- Date Issued
- 2019
- Authors
- Advisors
- Series
- Topics
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- Alzheimer's disease Serial block-face scanning electron microscopy (SBEM)
- Big data
- Capstone projects
- CDeep3M
- Cell Image Library (CIL)
- Convolutional Neural Network (CNN)
- Data Science & Engineering Master of Advanced Study (DSE MAS)
- DeepEM3D
- Menbranes
- Mitochondria
- MultiResUnet
- Neural networks (Computer science)
- Nuclei
- P100 latency
- Vesicles
Formats
View formats within this collection
- Identifier
- Related Resources
- Cell Image Library CDeep3M: http://cellimagelibrary.org/cdeep3m
- Subset of large dataset from CIL used in this project is kept in Dropbox here: https://www.dropbox.com/sh/jmkhekzo1p4owbp/AACzKqSC8stOsWowNahxI6Osa?dl=0
Source data
Other resource
- License
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Creative Commons Attribution 4.0 International Public License
- Rights Holder
- Singhal, Tushar; Kolkur, Prashant
- Copyright
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Under copyright (US)
Use: This work is available from the UC San Diego Library. This digital copy of the work is intended to support research, teaching, and private study.
Constraint(s) on Use: This work is protected by the U.S. Copyright Law (Title 17, U.S.C.). Use of this work beyond that allowed by "fair use" or any license applied to this work requires written permission of the copyright holder(s). Responsibility for obtaining permissions and any use and distribution of this work rests exclusively with the user and not the UC San Diego Library. Inquiries can be made to the UC San Diego Library program having custody of the work.
- Digital Object Made Available By
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Research Data Curation Program, UC San Diego, La Jolla, 92093-0175 (https://lib.ucsd.edu/rdcp)
- Last Modified
2023-06-30