| Both sides previous revision
Previous revision
Next revision
|
Previous revision
|
main:sample [2017/10/25 20:43]
yli |
main:sample [2018/02/09 16:41]
yli [View sample description and DC frequencies] |
| <WRAP group> | <WRAP group> |
| <WRAP half column> | <WRAP half column> |
| * **Specify a unique ID for the new sample**\\ A name for the sample to be created. This identifier will appear under “identity” within the list of samples in the [[main:maingui | main GUI]]. Click the "Use name of directory" button to populate the unique ID field using the sample directory name. This can be done automatically if desired each time a sample is created by modifying the setting [Settings (menu bar) → ADCI Preferences -> Prepopulate sample ID using name of directory containing metaphase images].\\ Physical dose of the sample can be embedded in its ID, which may be recognized by ADCI automatically. Embedded physical dose has to be in the format of #Gy. For example, a 0.25 Gy sample generated on Oct 25th can be named as 'Oct25-0.25Gy', 'Oct25 S 025 GY' or 'Oct25Sample0_25 gy'. If it is named as 'Oct25 025Gy', ADCI will receive its dose incorrectly as 2.5025 Gy. Use a character other than space or underscore to separate dose from prefix. | * **Specify a unique ID for the new sample**\\ A name for the sample to be created. This identifier will appear under “identity” within the list of samples in the [[main:maingui | main GUI]]. Click the "Use name of directory" button to populate the unique ID field using the sample directory name. This can be done automatically if desired each time a sample is created by modifying the setting [Settings (menu bar) → ADCI Preferences -> Prepopulate sample ID using name of directory containing metaphase images].\\ Physical dose of the sample can be embedded in its ID, which may be recognized by ADCI automatically. Embedded physical dose has to be in the format of #Gy. For example, a 0.25 Gy sample generated on Oct 25th can be named as 'Oct25-0.25Gy', 'Oct25 S 025 GY' or 'Oct25Sample0_25 gy'. If it is named as 'Oct25 025Gy', ADCI will receive its dose incorrectly as 2.5025 Gy. Use a character other than space or underscore to separate dose from prefix. |
| | <WRAP round important>Please note the ID of a sample cannot be easily changed after it is created. If the sample ID must be modified, a "workaround" is described below under the heading "Rename a sample". </WRAP> |
| * **Directory metaphase images**\\ Cannot be modified. Displays the directory selected in the directory selection step. | * **Directory metaphase images**\\ Cannot be modified. Displays the directory selected in the directory selection step. |
| * **Description of the sample (Optional)**\\ Description is optional and is not required to be formatted in any specific way. The content within the description of a sample is simply displayed when the sample is highlighted in the [[main:maingui | main GUI]] and is not used in any calculation. Preset text within the description such as "Laboratory source", "Patient info", etc. may be filled in or removed entirely if desired. "Laboratory source" is prepopulated based on the content of [Settings (menu bar) → ADCI Preferences -> Laboratory Name]. "Sample import date" defaults to the current date. | * **Description of the sample (Optional)**\\ Description is optional and is not required to be formatted in any specific way. The content within the description of a sample is simply displayed when the sample is highlighted in the [[main:maingui | main GUI]] and is not used in any calculation. Preset text within the description such as "Laboratory source", "Patient info", etc. may be filled in or removed entirely if desired. "Laboratory source" is prepopulated based on the content of [Settings (menu bar) → ADCI Preferences -> Laboratory Name]. "Sample import date" defaults to the current date. If multiple samples derived from the same individual are present, it may be desirable to record the sample IDs of the other samples associated with the individual within the description of newly created samples. |
| * **Number of metaphases**\\ Cannot be modified. Reports the number of TIFF image files found in the new sample directory. | * **Number of metaphases**\\ Cannot be modified. Reports the number of TIFF image files found in the new sample directory. |
| * **List of metaphases in the sample**\\ Cannot be modified. A list of TIFF image files found in the new sample directory. | * **List of metaphases in the sample**\\ Cannot be modified. A list of TIFF image files found in the new sample directory. |
| |
| In the event of an unexpected shutdown during sample processing, samples are of course not saved in the normal manner. However, some samples which completed processing before the shutdown may be [[main:samplerecovery | recoverable]] if multiple samples were processed in the [[main:processqueue | process queue]]. For more information on recovering unsaved samples, consult the [[main:samplerecovery | sample recovery]] page. | In the event of an unexpected shutdown during sample processing, samples are of course not saved in the normal manner. However, some samples which completed processing before the shutdown may be [[main:samplerecovery | recoverable]] if multiple samples were processed in the [[main:processqueue | process queue]]. For more information on recovering unsaved samples, consult the [[main:samplerecovery | sample recovery]] page. |
| | |
| |
| ===== Edit sample description ===== | ===== Edit sample description ===== |
| To edit the description of an existing sample, highlight the appropriate sample within the Sample list in the [[main:mainGUI | main GUI]] and click the {{file:icon:file_edit.png?nolink&20}} icon. A dialog will appear similar to the dialog which was used to create the sample. The sample description can be modified under the heading "Description of the sample (Optional)". After modifications to the description have been completed, click "OK" and the new description will be saved. | To edit the description of an existing sample, highlight the appropriate sample within the Sample list in the [[main:mainGUI | main GUI]] and click the {{file:icon:file_edit.png?nolink&20}} icon. A dialog will appear similar to the dialog which was used to create the sample. The sample description can be modified under the heading "Description of the sample (Optional)". After modifications to the description have been completed, click "OK" and the new description will be saved. |
| | |
| | ===== Rename a sample ===== |
| | Once a sample has been created its sample ID cannot be changed. This is because ADCI assumes sample IDs are unchanging and IDs are used to "link" a sample with its associated contour files. When a sample is saved, a file is created with the extension ".adcisample". Note that this file name is unrelated to the sample ID. The file name can be changed arbitrarily as long as the extension remains ".adcisample", however changing the file name has no effect on the sample ID or ADCI in general. |
| | |
| | If a sample ID must be changed, you must create a new sample using the same images as the old sample, provide the desired sample ID during sample creation, and process the new sample. The content of the two ADCI samples should now be identical, however the newly created sample will have the desired ID. Please note, any previously generated reports containing the old sample will not be updated with the new sample ID. If this is an issue, we suggest providing the ID of the old sample within the description field of the new sample. In this manner, newly generated reports will display the description of the new sample, providing a method to locate the sample in older reports which contain the previous sample ID. |
| |
| ===== Process a sample ===== | ===== Process a sample ===== |
| * **DC/Cell (All)**\\ Number of DCs in all metaphase images found in the "Metaphase Images Path" directory divided by the total number of images in the "Metaphase Images Path". | * **DC/Cell (All)**\\ Number of DCs in all metaphase images found in the "Metaphase Images Path" directory divided by the total number of images in the "Metaphase Images Path". |
| * **DC/Cell (Range)**\\ Number of DCs in all metaphase images found in the "Metaphase Images Path" directory which have not been excluded by an [[main:imageselectionmodel | image selection model]] or through manual exclusion in the [[main:metaphaseimgviewer | metaphase image viewer]] divided by the total number of images which have not been excluded by an [[main:imageselectionmodel | image selection model]] or through manual exclusion in the [[main:metaphaseimgviewer | metaphase image viewer]]. | * **DC/Cell (Range)**\\ Number of DCs in all metaphase images found in the "Metaphase Images Path" directory which have not been excluded by an [[main:imageselectionmodel | image selection model]] or through manual exclusion in the [[main:metaphaseimgviewer | metaphase image viewer]] divided by the total number of images which have not been excluded by an [[main:imageselectionmodel | image selection model]] or through manual exclusion in the [[main:metaphaseimgviewer | metaphase image viewer]]. |
| | |
| | =====Export DC results and filtering stats to a comma-separated file===== |
| | Results of a processed samples can exported to a comma-separated-values(.csv) file to be analyzed in other tools. Simply highlight the sample and click the {{file:icon:mail_write.png?nolink&20}} icon. |
| | \\ Only selected images will be included in the .csv file. Each row in the file represents an image. The file have 19 columns, which are image path, DC counts for sigma 0.8 to sigma 1.8, total object count, segmented object count, length-width ratio value, centromere density value, finite difference value, classified object count and classified object ratio. |
| | |
