====== ADCI wiki table of contents ====== 
Welcome to the Automated Dicentric Chromosome Identifier and Radiation Dose Estimator (ADCI) software wiki. To return to this table of contents at any time, click the Cytognomix logo or the text "ADCI" at the top of any wiki page. Also note you can return to previous pages you have visited by clicking a link in the "trace" section above. While viewing offline in PDF format, the document contains bookmarks allowing navigation. 

If this is your first time using the software, the [[main:dongle | dongle]] and [[main:securitysplashscreen | splash screen]] pages will help get the software up and running. Next you may wish to consult the [[main:quickstart | quick start]] guide for a basic overview of the software and an example if its basic usage. The [[main:mainGUI | main GUI]] page provides and overview of the graphical user interface and can help you to locate the tools necessary to use the software.

ADCI Online is a cloud-based implementation of ADCI. Briefly, metaphase cell images to be analyzed are uploaded to cloud storage, then ADCI is executed remotely using a web browser. ADCI Online extends the capacity of a physical workstation with ADCI installed, and can fulfill "burst" requirements for analysis of large numbers of samples using parallelized cloud-based instances. See the heading "ADCI Online" below for additional details. As of ADCI version 1.13, cloud storage can be accessed directly through ADCI Desktop.

===== Peer-reviewed publications =====
[[public:references | ADCI patents and full publication list]]\\ 
[[https://www.jove.com/video/56245/expedited-radiation-biodosimetry-automated-dicentric-chromosome | Video overview of ADCI published in the Journal of Visualized Experiments]]\\ 

===== ADCI Online =====
[[adcionline:overview | overview ]]\\ 
[[adcionline:cloudstorage | interact with cloud storage using a web browser]]\\ 
[[adcionline:cloudstoragedesktop | interact with cloud storage using ADCI (requires ADCI Desktop v1.13)]]\\ 
[[adcionline:accesssystem | access ADCI_Online and begin streaming session]]\\ 
[[adcionline:interacting | interact with ADCI_Online (recommendations and additional explanation)]]

===== ADCI =====
==== Getting started ====
[[main:demoversion | demonstration version]]\\ 
[[main:installation | installation]]\\ 
[[main:quickstart | quick start]]\\ 
[[main:dongle | dongle]]\\ 
[[main:securitysplashscreen | splash screen]]\\ 
[[main:maingui | main GUI]]\\ 
[[main:console | console]]\\ 
[[main:plots | plots]]

==== Samples ====
[[main:sample | sample]]\\ 
[[main:processedsample | processed sample]]\\ 
[[main:imageselectionmodel | image selection model]]\\ 
[[main:presetimgselectionmodels | preset image selection models]]\\ 
[[main:selectionmodelsearch | automated search for optimal image selection models]]\\
[[main:processqueue | process queue]]\\ 
[[main:gpuacceleration | process samples with GPU]]\\ 
[[main:metaphaseimgviewer | metaphase image viewer]]\\ 
[[main:svmsigma | SVM sigma value]]\\ 
[[main:fpfilters | false positive filters]]\\ 
[[main:groupbinmethod | group bin method]]\\ 
[[main:qualitycontrol | quality control]]\\ 
[[main:processtime | time required to process samples]]\\ 
[[main:samplepackunpack | transfer sample to another computer (pack/unpack sample)]]\\ 
[[main:combinesamples | combine processed samples]]

==== Estimate dose ====
[[main:curvecalibrationwizard | curve calibration wizard]]\\ 
[[main:doseestimationwizard | dose estimation wizard]]\\ 
[[main:calibrationcurve | calibration curve]]\\ 
[[main:estimatedose | estimate dose]]\\ 
[[main:partialbodyestimatedose | partial-body dose estimation]]\\ 
[[http://adciwiki.cytognomix.com/files/resources/guide_to_manually_derived_calibration_curves.pdf | guide to create manually derived calibration curves (pdf)]]

==== Reports ====
[[main:report | report]]\\ 
[[main:samplereport | sample report]]\\ 
[[main:curvereport | calibration curve report]]\\ 
[[main:dosereport | dose estimation report]]\\ 
[[main:csvdosereport | provider report (dose estimation - csv format)]]\\
[[main:optimalselectionsearchreport | optimal image selection model search report]]

==== Execution history ====
[[main:logfile | log file]]\\ 
[[main:adcilogviewer | ADCI log file viewer]]\\ 
[[main:logviewersidebar | log viewer sidebar]]\\ 
[[main:viewertab | viewer tab]]\\ 
[[main:searchtab | search tab]]\\ 
[[main:integritytab | integrity tab]]\\ 
[[main:samplerecovery | sample recovery]]

===== Other =====
[[http://adciwiki.cytognomix.com/files/resources/ADCI_ShortcutDocument.pdf | Shortcut Document - Overview of ADCI software icons and main concepts (pdf)]]\\ 
[[main:settingsandprefs | settings and preferences]]\\ 
[[main:faqandtips | FAQ, useful tips and tricks]]\\
[[bgq:startpage | View ADCI-BGQ wiki pages (in progress)]]\\ 
[[main:abbreviations | abbreviations]]\\ 
[[main:acknowledgements | acknowledgements]]\\ 
[[public:contactus | contact us]]\\