====== Quick start ======
This guide first provides a high-level overview of the ADCI software and a brief sample workflow.

===== High-level overview =====
The main functionality of this software is to process groups of metaphase images called [[main:sample | samples]], count the number of dicentric chromosomes in each image using image processing techniques, and return the estimated radiation dose of samples in Gray (Gy). Two types of samples are necessary: 1) calibration samples and 2) test samples. The physical dose (in Gy) of calibration samples are known before any interaction with the software and are used to generate a [[main:calibrationcurve | calibration curve]]. In test samples the physical dose is unknown and is [[main:estimatedose | estimated]] by comparing dicentric chromosome frequency in a [[main:processedsample | processed]] test sample with the calibration curve.

===== Sample workflow of main software elements =====
We present a sample workflow of the main elements of the software. You may wish to familiarize yourself with the layout of ADCI [[main:mainGUI | graphical user interface (GUI)]] before continuing. 

==== Open ADCI software ====
Related pages: [[main:dongle | dongle]] | [[main:securitysplashscreen | startup splash screen]]

==== Create or open sample ====
Related page: [[main:sample | sample]]

If a calibration curve has not previously been generated, at least three calibration samples (known Gy) must be created/opened. The only exception to this is if you intend to generate a calibration curve by manually entering curve coefficients. Additionally, at least one test sample (unknown Gy) file must be created/opened to perform dose estimation.

==== Process sample ====
Related pages: [[main:sample | sample]] | [[main:processedsample | processed sample]] | [[main:processqueue | process queue]]

__Add sample to ADCI Process Queue__\\ Samples created in the previous step must be processed in order to obtain dicentric counts in each sample. If a saved sample was opened, it has already been processed. To check if a sample has been processed, observe the list of samples in the [[main:mainGUI | mainGUI]] under the heading "Processed". Unprocessed samples must be added to the ADCI Process Queue for processing. To do so, highlight an unprocessed sample and click the {{file:icon:shoppingcart_add.png?nolink&20}} icon. 

__Process samples within the ADCI Process Queue__\\ Items in the process queue can be processed individually by highlighting an item in the process queue and clicking the {{file:icon:player_play.png?nolink&20}} icon. All items currently in the process queue can be processed sequentially in one click by clicking the {{file:icon:player_fastforward.png?nolink&20}} icon.


==== Create curve ====
Related pages: [[main:calibrationcurve | calibration curve]] | [[main:curvecalibrationwizard | calibration curve wizard]] | [[main:sample | sample]] | [[main:processedsample | processed sample]]

The [[main:curvecalibrationwizard | calibration curve wizard]] simplifies the process of creating a calibration curve. It is recommended to use the wizard unless you intend to manually enter curve coefficients. 

==== Estimate dose ====
Related pages: [[main:estimatedose | dose estimation]] | [[main:partialbodyestimatedose | partial-body dose estimation]] | [[main:doseestimationwizard]] | [[main:calibrationcurve | calibration curve]] | [[main:sample | sample]] | [[main:processedsample | processed sample]]

The [[main:doseestimationwizard | dose estimation wizard]] simplifies the process of performing [[main:estimatedose | estimating dose]] based on existing processed test sample(s) and calibration curve.

==== Interpret dose estimation results ====
Related pages: [[main:estimatedose | dose estimation]] | [[main:console]] | [[main:calibrationcurve | calibration curve]] | [[main:sample | sample]] | [[main:processedsample | processed sample]]

Dose estimation results are visible in the [[main:console | console]]. Estimated radiation dose in Gy can be found in dose estimation results under the heading "Dose by [curvename]" where [curvename] is the ID of the calibration curve used in the dose estimation. For a more detailed description of fields in dose estimation results consult the [[main:estimatedose | dose estimation]] page.