NDLI: (3) The CellOrganizer project: An open source system to learn image-derived models of subcellular organization over time and space

Content Provider	IEEE Xplore Digital Library
Author	Murphy, R.F.
Copyright Year	2012
Description	Author affiliation: Lane Center for Computational Biology and Department of Biological Sciences Carnegie Mellon University, Pittsburgh, Pennsylvania, USA (Murphy, R.F.)
Abstract	The CellOrganizer project (http://cellorganizer.org) provides open source tools for learning generative models of cell organization directly from images and for synthesizing cell images (or other representations) from one or more of those models. Model learning captures variation among cells in a collection of images. Images used for model learning and instances synthesized from models can be two- or three-dimensional static images or movies. Current components of CellOrganizer can learn models of cell shape, nuclear shape, chromatin texture, vesicular organe lie number, size, shape and position, and microtubule distribution. These models can be conditional upon each other: for example, for a given synthesized cell instance, organelle position will be dependent upon the cell and nuclear shape ofthat instance. The models can be parametric, in which a choice is made about an explicit form to represent a particular structure, or non-parametric, in which distributions are learned empirically. One of the main uses of the system is in support of cell simulations: models learned from separate experiments can be combined into one or more synthetic cell instances that are output in a form compatible with cell simulation engines such as MCell, Virtual Cell and Smoldyn. Another important application of the system is in comparison of target patterns and perturbagen effects in high content screening and analysis. This is currently done using numerical features, but these are difficult to compare across different microscope systems or cell types since features can be affected by changes in more than one aspect of cell organization. More robust comparisons can be made using generative model parameters, since these can distinguish effects on cell size or shape from effects on organelle pattern. Ultimately, it is anticipated that collaborative efforts by many groups will enable creation of image-derived generative models that permit accurate modeling of cell behaviors, and that can be used to drive experimentation to improve them through active learning.
Starting Page	1
Ending Page	2
File Size	1244125
Page Count	2
File Format	PDF
ISBN	9781467325592
e-ISBN	9781467325608
e-ISBN	9781467325585
DOI	10.1109/BIBM.2012.6392673
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2012-10-04
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Shape Biological system modeling Computational modeling Organizations Educational institutions Computational biology
Content Type	Text
Resource Type	Article

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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