ADCI Wiki main

main:abbreviations

Anonymous (anonymous@undisclosed.example.com) — 2017-04-18T14:07:43+00:00

Abbreviations ADCI Automated Dicentric Chromosome Identifier ADCIDE Automated Dicentric Chromosome Identifier and Radiation Dose Estimator DC Dicentric chromosome FP False positive dicentric chromosome MC Monocentric chromosome ML Machine learning

main:acknowledgements

Anonymous (anonymous@undisclosed.example.com) — 2018-06-08T19:25:54+00:00

Acknowledgements Icons used in this software: * Simplicio by Neurovit * the Oxygen Iconset by the Oxygen team * Medical Icons by MedicalWP. ADCI uses * Qt libraries under LGPL license. License information and source code can be found here. *

main:adcilogviewer

Anonymous (anonymous@undisclosed.example.com) — 2017-03-08T16:01:52+00:00

ADCI Log Viewer This supplemental log viewing software has been bundled with the main ADCI product. It is meant to simplify examination of log files and allows the user to: * View log files * Search all log files or a subset of log files * Perform an automated examination of log files to determine if an operation ended unexpectedly and locate samples which were not processed successfully due to the unsuccessful operation.

main:bgqlocationdisplaykriginganddensificationonmultiplesamplesetsofanarea

Anonymous (anonymous@undisclosed.example.com) — 2018-10-29T20:54:18+00:00

Location display, Kriging and densification on multiple sample sets of an area In the ADCI-BGQ workflow, if two or more iterations were performed on an area, then multiple sample sets were generated, each of which came from one iteration. Therefore, at the end of the current iteration, you should perform Kriging on all sample sets of the are at the same time.

main:calibrationcurve

Anonymous (anonymous@undisclosed.example.com) — 2019-06-26T16:28:48+00:00

Calibration curve Despite the use of a common set of laboratory protocols, the dose calibration curves produced from each laboratory are unique and may produce different dose estimates . To determine DC counts and ensure internally consistent dose estimates, test samples and calibration curves from the same laboratory should both be processed using ADCI software. A calibration curve is required to perform

main:combinesamples

Anonymous (anonymous@undisclosed.example.com) — 2020-09-15T20:34:05+00:00

Combine processed samples Feature present since ADCI version 1.12. Overview If it is necessary to combine two processed samples, one approach would be to copy all images associated with both samples into a directory, create a new sample, then process the new sample. However, when a

main:console

Anonymous (anonymous@undisclosed.example.com) — 2017-05-23T19:50:08+00:00

Console The console is an element of the main GUI. Data appears in the console when a sample or a curve is highlighted in the main GUI and when operations have completed such as dose estimation. The console displays information in real-time, while reports can be used to save information related to

main:csvdosereport

Anonymous (anonymous@undisclosed.example.com) — 2020-09-15T15:18:59+00:00

Provider report (dose estimation - csv format) Feature present since ADCI version 1.4. A provider report is a report containing sample descriptions and information related to a previously performed dose estimation. A provider report organizes dose estimation output in comma separated values (CSV) format. Its intended purpose is to aid users in the creation of a report which can be sent to a health care provider. Values can be easily copied and pasted from spreadsheet software into a laborato…

main:curvecalibrationwizard

Anonymous (anonymous@undisclosed.example.com) — 2017-10-25T20:55:10+00:00

Curve calibration wizard This wizard guides the user through the process of generating a calibration curve based on processed calibration samples. The wizard consists of a series of screens. To move forward to the next screen click “Next”, and previous screens can be viewed and edited by clicking the arrow on the top left of the wizard dialog.

main:curvereport

Anonymous (anonymous@undisclosed.example.com) — 2017-03-06T19:06:57+00:00

Calibration curve report A calibration curve report is a report containing information related to one or more calibration curves. Content A curve report contains the following content: * Single plot containing all selected calibration curves. A plot legend is located below the plot.

main:demoversion

Anonymous (anonymous@undisclosed.example.com) — 2017-08-25T20:59:54+00:00

Demonstration version A demonstration version (demo) of ADCI is available at and can be downloaded at no cost. It is bundled with a built-in sample and several calibration curves (described in our F1000Research paper) allowing you to become familiar with core ADCI functionality such as image selection, dose estimation, and report creation. The demonstration version can carry out many functions present in the commercial product, except for sample processing and…

main:dongle

Anonymous (anonymous@undisclosed.example.com) — 2021-11-02T19:39:02+00:00

Dongle ADCI software requires the presence of a dongle to run. If the software expiry date present within the dongle is in the future, ADCI software will allow access to the program. Using the dongle To use the dongle, simply plug the dongle into a USB port on your computer. Please ensure the dongle is plugged in before loading the software. If the dongle is not present, an error message will be presented within the

main:doseestimationwizard

Anonymous (anonymous@undisclosed.example.com) — 2017-04-10T14:31:56+00:00

Dose estimation wizard This wizard guides the user through the process of estimating radiation dose based on calibration curve and one or more test samples. The wizard consists of a series of screens. To move forward to the next screen click “Next”, and previous screens can be viewed and edited by clicking the arrow on the top left of the wizard dialog.

main:dosereport

Anonymous (anonymous@undisclosed.example.com) — 2018-01-26T17:05:23+00:00

Dose estimation report A dose estimation report is a report containing information related to a previously performed dose estimation. Content A dose estimation report contains the following content: * Description of calibration curves present in dose estimation *

main:estimatedose

Anonymous (anonymous@undisclosed.example.com) — 2018-02-02T15:48:58+00:00

Estimate dose For most purposes, the end goal of ADCI software is to provide the estimated radiation dose (in Gy) of test samples. In order to generate the estimated dose, processed samples and a calibration curve must be present. Alternatively, dose estimation can also be performed on dicentric frequency alone without the presence of a curve.

main:faqandtips

Anonymous (anonymous@undisclosed.example.com) — 2018-06-26T19:26:15+00:00

FAQ, tips and tricks This page answers frequently asked questions and provides some useful tips and tricks in ADCI. FAQ What does it mean when the software says "some DC frequencies have poor quality. Do you want to continue?" This warning will appear during

main:fpfilters

Anonymous (anonymous@undisclosed.example.com) — 2017-04-04T02:20:50+00:00

False positive filters False positive (FP) filters are a second layer of scrutiny which can be automatically applied to chromosomes determined by ADCI to be dicentric. When a dicentric chromosome meets the threshold for a FP filter, it will no longer be classified as dicentric for the purposes of dose estimation and will have a yellow contour in the

main:gpuacceleration

Anonymous (anonymous@undisclosed.example.com) — 2020-06-01T19:04:35+00:00

Process Sample with GPU Feature present since ADCI version 1.11. Introduction ADCI is capable of GPU computing during sample processing, under the following conditions. ADCI uses CUDA to perform general-purpose GPU computing. It requires a NVIDIA video card (GPU) with computing capability 2.0 or higher.

main:groupbinmethod

Anonymous (anonymous@undisclosed.example.com) — 2017-05-10T14:22:55+00:00

Group bin method Brief overview Group bin distance is a novel measure of image quality based on a comparison between observed chromosomes lengths in an image with chromosome lengths obtained from the human genome sequence. Observed chromosome lengths are approximated by computing the chromosome area in pixels as actual chromosome length is difficult to measure accurately in images. Chromosomes are then assigned to one of three categories made up of seven chromosome groups

main:imageselectionmodel

Anonymous (anonymous@undisclosed.example.com) — 2017-11-09T18:44:07+00:00

Image selection model An image selection model is a series of filters which exclude undesirable images within a sample from use in calibration curve generation or dose estimation. Excluded images are still present in the sample and can be viewed in the metaphase image viewer within which they can be manually re-included.

main:installation

Anonymous (anonymous@undisclosed.example.com) — 2018-06-06T21:27:52+00:00

Installation of ADCI Software ADCI software is released in a binary installation package file. The latest release is version 1.11. The installation file is named ADCI_Setup1.11.r_x64.exe (ADCI_Setup1.11.r_x86.exe if you requested a 32-bit version of ADCI). You can find this file in the USB flash drive shipped by Cytognomix.

main:integritytab

Anonymous (anonymous@undisclosed.example.com) — 2017-03-08T16:10:00+00:00

Integrity tab The Integrity tab is a tab present in the ADCI Log Viewer supplemental software. Populating integrity tab This tab is populated when a search is performed within the search tab. Note the “Perform integrity check” checkbox must be checked in the search tab in order for the integrity tab to be populated.

main:logfile

Anonymous (anonymous@undisclosed.example.com) — 2017-06-22T19:51:10+00:00

ADCI log file Log files are automatically generated and contain operations executed by the ADCI software. Log files can be used to keep track of operations previously performed and to locate the point of failure if an unexpected shutdown of the software occurs.

main:logviewersidebar

Anonymous (anonymous@undisclosed.example.com) — 2017-03-08T16:05:25+00:00

ADCI Log Viewer sidebar A sidebar is located on the left side of the log viewer window which contains the names of all log files found in the current directory. If no log files are present in the sidebar, click “File” and choose “Select log file directory

main:maingui

Anonymous (anonymous@undisclosed.example.com) — 2017-01-30T20:31:28+00:00

Main GUI When ADCI software is loaded, the graphical user interface (GUI) shown below is presented. Five major areas of the GUI are denoted by green numbers within circles and are each briefly described in this page. Note each section has a dedicated page, the link to which can be found in each section's brief description.

main:metaphaseimgviewer

Anonymous (anonymous@undisclosed.example.com) — 2018-01-23T21:18:04+00:00

Metaphase image viewer The metaphase image viewer is accessed by first highlighting a processed sample in the list of samples within the mainGUI, then clicking the icon. Meaning of coloured contours After sample processing, the software outlines each processed chromosome in a metaphase cell in color. Objects without outlines represent overlapped chromosomes, nuclei and debris, which are not included in counts of objects in a cell. Coloured contours represent the following:

main:optimalselectionsearchreport

Anonymous (anonymous@undisclosed.example.com) — 2018-02-09T16:55:42+00:00

Optimal image selection search report After finishing an optimal image selection model search (same as image selection model optimization), users can summarize the search by generating an optimal image selection search report. The report records the search configuration such as evaluation method and optimal image selection model result. Users can specify which optimal models found in the search to be included in the report.

main:partialbodyestimatedose

Anonymous (anonymous@undisclosed.example.com) — 2020-10-13T15:10:33+00:00

Partial-body dose estimation Feature present since ADCI version 1.12. Manuscript presenting the partial-body algorithm in ADCI: Direct link to pdf Enable partial-body dose estimation Partial-body dose estimation can be performed on processed test samples. It can be enabled by first executing the

main:plots

Anonymous (anonymous@undisclosed.example.com) — 2018-02-08T16:25:36+00:00

Plots A variety of plots are available in ADCI software. Dose estimation automatically generates a plot upon execution, while the other plots are generated upon request. Zoom and pan functionality Feature present since ADCI version 1.9 Zoom Zoom in and out using the mouse wheel. Note the zoom functionality zooms in on both the x and y axis. Plot axes are rescaled as necessarily while zooming. The default level of zoom ensures all data points are contained within the visible area (viewport)…

main:presetimgselectionmodels

Anonymous (anonymous@undisclosed.example.com) — 2017-05-16T16:24:02+00:00

Preset image selection models ADCI includes several preset image selection models. These image selection models are available for use directly after installation and do not have to be manually designed. Depending on which types of image quality issues are most prevalent in a sample, one of the preset models may be most appropriate to address those specific issues. This page will be updated with additional filters and filter descriptions which will aid the process of choosing the most appropria…

main:processedsample

Anonymous (anonymous@undisclosed.example.com) — 2017-01-25T21:29:19+00:00

Processed sample A processed sample is a sample which has been processed by ADCI software through the ADCI Process Queue. When a sample is processed, metaphase images are segmented and dicentric chromosomes are counted at a variety of SVM sigma values. These dicentric counts are used when generating

main:processqueue

Anonymous (anonymous@undisclosed.example.com) — 2021-11-02T19:52:00+00:00

ADCI Process Queue ADCI software processes samples using a queue system within which one sample is processed at a time. To add a sample to the process queue, highlight an unprocessed sample within the main GUI and click the icon. Items in the process queue can be processed individually by highlighting an item in the process queue and clicking the

main:processtime

Anonymous (anonymous@undisclosed.example.com) — 2017-05-12T19:39:11+00:00

ADCI sample process time These benchmarks were obtained using an MSI Leopard Pro laptop running Windows 10. The laptop has an i7-6700HQ processor and 16GB DDR4 RAM. Total images Image dimensions (pixels) Image source Process time (min) Images processed per second

main:qualitycontrol

Anonymous (anonymous@undisclosed.example.com) — 2017-08-08T15:08:37+00:00

Quality control This functionality will become available in version 1.4 of ADCI. Quality control (QC) metrics are applied to samples and aberrations. QC issues related to samples are visible in the sample list within the main GUI. Samples which do not meet QC thresholds are marked with an orange or yellow background color in the sample's

main:quickstart

Anonymous (anonymous@undisclosed.example.com) — 2020-09-15T18:00:13+00:00

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 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 cali…

main:report

Anonymous (anonymous@undisclosed.example.com) — 2017-06-19T21:28:33+00:00

Report An ADCI report is an HTML file containing text, tabular data, and images related to the report subject. Reports are generated by clicking “Reports” in the menu bar of the main GUI and selecting a report type. The following types of reports are available:

main:sample

Anonymous (anonymous@undisclosed.example.com) — 2018-02-09T16:41:36+00:00

Sample A sample is a collection of TIFF image files (.tif or .tiff extension) of metaphase cells stored in a directory. Samples must be processed to become processed samples before they can be used to generate calibration curves or as test samples to estimate radiation dose. The steps necessary to process a sample can be found on the

main:samplepackunpack

Anonymous (anonymous@undisclosed.example.com) — 2017-08-25T19:57:47+00:00

Pack/unpack sample This feature is present in ADCI v1.5 or newer In the event a sample must be moved from one computer to another, multiple components of the sample must be transferred to the destination computer. Sample packing/unpacking provides functionality to simplify this process.

main:samplerecovery

Anonymous (anonymous@undisclosed.example.com) — 2017-01-31T21:49:12+00:00

Processed sample recovery file In the event of an unexpected shutdown or other error while executing ADCI software before processed samples can be saved, some samples may be fully processed and able to be recovered without processing them again. Location and duration of recovery files

main:samplereport

Anonymous (anonymous@undisclosed.example.com) — 2017-03-06T19:06:44+00:00

Sample report A sample report is a report containing information related to one or more samples. Content A sample report contains the following content: * Table of contents * General overview of samples * Dicentric distribution related plots and tables

main:searchtab

Anonymous (anonymous@undisclosed.example.com) — 2017-03-08T16:08:03+00:00

Search tab The Search tab is a tab present in the ADCI Log Viewer supplemental software. Performing a search To perform a search, click the Search tab above the ADCI Log Viewer main window area. Searches can be performed based on a number of search criteria described below. If multiple criteria are specified, lines within the

main:securitysplashscreen

Anonymous (anonymous@undisclosed.example.com) — 2021-11-02T19:40:31+00:00

ADCI splash screen When ADCI software is opened, a splash screen will appear and must be interacted with before the main window can be accessed. The splash screen acts as an entry point to the software ensuring both the dongle is connected and the subscription is active before allowing access. If both checks are successful, an

main:selectionmodelsearch

Anonymous (anonymous@undisclosed.example.com) — 2018-02-09T15:57:29+00:00

Automated Search for Optimal Image Selection Models This feature is present in ADCI v1.7 or newer The total number of potential image selection models is unlimited and effective image selection model configurations differ between laboratories due to their laboratory specific

main:settingsandprefs

Anonymous (anonymous@undisclosed.example.com) — 2020-06-01T20:12:02+00:00

Settings and Preferences Settings Menu Access settings dialogs for many aspects of ADCI in the settings menu, located at the top of the main GUI. ADCI preferences False positive filters Image selection model optimization Partial-body * Expected baseline DC frequency for an unirradiated sample

main:svmsigma

Anonymous (anonymous@undisclosed.example.com) — 2017-03-08T15:43:19+00:00

SVM sigma value The SVM sigma value, referred to as “σ”, is an SVM tuning parameter and effectively represents a tradeoff between increased sensitivity and reduced specificity in dicentric chromosome (DC) detection. Simply put, a higher SVM sigma value will generally find more dicentric chromosomes but will result in more false positives (FPs). A lower SVM sigma value will generally result in a lower FP rate but may miss true positives (TPs). This trade-off is depicted in the image below.

main:tableofcontents

Anonymous (anonymous@undisclosed.example.com) — 2021-11-22T20:12:08+00:00

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

main:viewertab

Anonymous (anonymous@undisclosed.example.com) — 2017-03-08T16:07:47+00:00

Viewer tab The Viewer tab is a tab present in the ADCI Log Viewer supplemental software. This tab is used to view the contents of log files in a tabular format. Populating viewer tab The tab can be populated directly by double clicking a log file in the sidebar or through links generated within search results generated in the