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main:faqandtips [2018/02/01 21:42]
bshirley
main:faqandtips [2018/06/26 19:26] (current)
bshirley
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 ===== FAQ ===== ===== FAQ =====
-**What does it mean when the software says "some DC frequencies have poor quality. Do you want to continue?"**+=== 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:calibrationcurve | calibration curve generation]] or [[main:estimatedose | dose estimation]] if samples do not meet quality control thresholds. These thresholds are explained in [[main:qualitycontrol | the quality control page]] and can also be customized. When such a warning happens, users are encouraged to review their metaphase image data to see if there are excessive images of poor quality. If users are confident about their data or no better data can be obtained, users can ignore this warning.   This warning will appear during [[main:calibrationcurve | calibration curve generation]] or [[main:estimatedose | dose estimation]] if samples do not meet quality control thresholds. These thresholds are explained in [[main:qualitycontrol | the quality control page]] and can also be customized. When such a warning happens, users are encouraged to review their metaphase image data to see if there are excessive images of poor quality. If users are confident about their data or no better data can be obtained, users can ignore this warning.  
  
-**Can I change the name of a saved sample file or the ID of a sample in ADCI**+=== Can I change the name of a saved sample file or the ID of a sample in ADCI ===
  
 The ID of a sample is given by users when the sample is created. It cannot be changed after initialization. ADCI uses sample IDs to find contour files for samples and to reference samples in reports. The filenames of sample files (*.adcisample) can be changed arbitrarily. Changing its filename does not affect the sample ID saved in the file. When users are saving a sample to a file, ADCI will use the ID as the default filename. The ID of a sample is given by users when the sample is created. It cannot be changed after initialization. ADCI uses sample IDs to find contour files for samples and to reference samples in reports. The filenames of sample files (*.adcisample) can be changed arbitrarily. Changing its filename does not affect the sample ID saved in the file. When users are saving a sample to a file, ADCI will use the ID as the default filename.
  
-**Is there a way to view the optimal image selection models after it has been saved in the optimal model search and the search dialogue is closed** +=== Is there a way to view the optimal image selection models after it has been saved in the optimal model search and the search dialogue is closed === 
  
 Yes. Users can specify the destination folder when they are saving a optimal image selection model found in the search. By default, it will be the same folder of the preset models. Such models can be viewed in the same way as preset models, which is demonstrated in [[main:imageselectionmodel | this page]]. If the optimal models are saved in a different folder, they need to be moved to the folder of preset models to be viewed. Yes. Users can specify the destination folder when they are saving a optimal image selection model found in the search. By default, it will be the same folder of the preset models. Such models can be viewed in the same way as preset models, which is demonstrated in [[main:imageselectionmodel | this page]]. If the optimal models are saved in a different folder, they need to be moved to the folder of preset models to be viewed.
  
-**Is it necessary to keep image files associated with a sample stored on my computer after the sample has been processed** +=== Is it necessary to keep image files associated with a sample stored on my computer after the sample has been processed ===
  
 The presence of image files is not required for any [[main:processedsample | processed sample]] operations with the exception of viewing images in the [[main:metaphaseimgviewer | metaphase image viewer]]. Operations such as [[main:estimatedose | dose estimation]], [[main:calibrationcurve | calibration curve generation]], [[main:report | report generation]], etc. can all be performed if sample images are no longer present. If it is not necessary to view sample images in the metaphase image viewer, the images may be freely moved to another location or removed. This may be desirable due to the large amount of disk space some sets of images require. It is also possible to process a sample directly from an external drive without first copying images to a local drive. However, if this method is used, please note that images cannot be viewed in the metaphase image viewer when the external drive is disconnected. The presence of image files is not required for any [[main:processedsample | processed sample]] operations with the exception of viewing images in the [[main:metaphaseimgviewer | metaphase image viewer]]. Operations such as [[main:estimatedose | dose estimation]], [[main:calibrationcurve | calibration curve generation]], [[main:report | report generation]], etc. can all be performed if sample images are no longer present. If it is not necessary to view sample images in the metaphase image viewer, the images may be freely moved to another location or removed. This may be desirable due to the large amount of disk space some sets of images require. It is also possible to process a sample directly from an external drive without first copying images to a local drive. However, if this method is used, please note that images cannot be viewed in the metaphase image viewer when the external drive is disconnected.
  
-**Can create a calibration curve with multiple calibration samples of the same dose**+=== Should use wizards for calibration curve generation and dose estimation or is it better to enter values manually ===
  
-This is possible to do, but it does require the use of a "workaround". While [[main:calibrationcurve | generating a calibration curve]], duplicate dose values are disallowedThe "validate" button on the "Fit a curve" dialog will turn duplicate dose values red, thus preventing the completion of the dialog. To work around thisthe dose values of duplicate samples can be changed to a value very close to - but not identical to - its original value. For example if you would like to create a calibration curve containing two samples at 3Gy, one sample can keep its dose  value of 3 and the other can be changed to 3.0001. However, do not enter more than 7 digits after the decimal point in the new dose. ADCI will no longer flag the dose values as duplicated.+In almost all circumstances, it is preferable to use the [[main:curvecalibrationwizard calibration curve wizard]] when generating a [[main:calibrationcurve | calibration curve]] and the [[main:doseestimationwizard | dose estimation wizard]] to perform [[main:estimatedose | dose estimation]]We recommend exclusively using the wizards when using ADCI for the first timethen after you have become more familiar with ADCI functionality to manually enter values when/if specific functionality is required which the wizard cannot provideUsing wizards remove several potential sources of error such as the application of the appropriate [[main:imageselectionmodel | image selection model]] during dose estimation
  
 +=== Does ADCI require TIF images  ===
 +​​TIF​ images​ are preferred. We have also worked with jpeg images, however they exhibit loss of resolution due to their compression algorithm. The [[main:processtime | ADCI sample process time]] page shows the difference in resolution and speed of processing. The jpeg images are labelled 912x732 pixels in this page. Supported image formats are also discussed on the [[main:sample | sample]] page under the heading "Supported image formats".
 +
 +=== How many images should I prepare for each dose point ===
 +​The most important thing about the images ​i​s that they should contain exclusively or primarily metaphase cells. ADCI will process images that don't have metaphases, but the​se​ reduce the speed of processing and image selection​, and can affect the image selection criteria​. Typically​,​ more images ​(several thousand) ​are required at low dose than ​at ​high dose​ (500-1000)​. The system provides a warning about sample quality if there are fewer than 100 dicentric chromosomes detected in a sample (these are the criteria in the IAEA manual). This means that for calibration samples, 2000-3000 images will provide good confidence intervals. But it all depends on the quality of your data. If many images contain a lot of sister chromatid separation, then ADCI needs more images to find those images that show strong cohesion between chromatids. 
 +
 +=== Can I continue to use curves/samples generated using an older version of ADCI after upgrading to a new version ===
 +It is important to note dicentric detection may vary across ADCI versions. Reasons for this variation include dicentric detection algorithm upgrades and software bug fixes. It is therefore recommended to analyse both calibration and test samples using the same version of ADCI. 
  
 ===== Useful tips and tricks ===== ===== Useful tips and tricks =====
 +
 +==== Create a calibration curve using multiple samples of the same dose ====
 +
 +This is possible to do, but it does require the use of a "workaround". While [[main:calibrationcurve | generating a calibration curve]], duplicate dose values are disallowed. The "validate" button on the "Fit a curve" dialog will turn duplicate dose values red, thus preventing the completion of the dialog. To work around this, the dose values of duplicate samples can be changed to a value very close to - but not identical to - its original value. For example if you would like to create a calibration curve containing two samples at 3Gy, one sample can keep its dose  value of 3 and the other can be changed to 3.0001. However, do not enter more than 7 digits after the decimal point in the new dose. ADCI will no longer flag the dose values as duplicated.
 +
 ==== View outlier images ==== ==== View outlier images ====
 Quality statistics of a [[main:sample | sample]] can be visualized in the [[main:plots | plot]] display. Some outlier images may be present when viewing certain plots. It may be useful to view these outlier images, especially to review the quality of the image. The [[main:metaphaseimgviewer | metaphase image viewer]] in ADCI can sort images in a variety of different orders allowing users to find outlier images easily. Quality statistics of a [[main:sample | sample]] can be visualized in the [[main:plots | plot]] display. Some outlier images may be present when viewing certain plots. It may be useful to view these outlier images, especially to review the quality of the image. The [[main:metaphaseimgviewer | metaphase image viewer]] in ADCI can sort images in a variety of different orders allowing users to find outlier images easily.
main/faqandtips.1517521348.txt.gz · Last modified: 2018/02/01 21:42 by bshirley