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main:bgqcreateasampleforaperson [2018/10/29 19:08] rlu45 |
main:bgqcreateasampleforaperson [2021/02/09 16:28] bshirley removed |
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====== Create a sample for a person ====== | ====== Create a sample for a person ====== | ||
- | A sample is a compressed file of the .tgz (.tar.gzip) format, containing a number of metaphase images from the person. It is the basic unit for estimating the radiation dose that the person | + | A sample is a compressed file of the .tgz (.tar.gzip) format, containing a number of metaphase images from the person. It is the basic unit for estimating the radiation dose that the person |
===== Prepare ===== | ===== Prepare ===== | ||
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{{ file: | {{ file: | ||
- | First, you need to upload the metaphase images of the person to the BGQ server, which can be accomplished by the bottom | + | <WRAP group> |
- | In the right part, you can also create a new directory, rename | + | <WRAP half column> |
+ | First, you need to upload the metaphase images of the person to the BGQ server, which can be accomplished by the bottom | ||
+ | </ | ||
+ | <WRAP half column> | ||
+ | {{ file: | ||
+ | </ | ||
+ | </ | ||
+ | In the right part, you can also create a new directory, rename and delete a directory/ | ||
- | After uploading the metaphase images, you can create samples | + | After uploading the metaphase images, you can create samples |
- | Then the paths of all selected directories will be displayed in the drop-down list. For the source directory currently being displayed | + | {{ file: |
+ | |||
+ | Then the paths of all selected directories will be displayed in the drop-down list. For the source directory currently being selected | ||
* ‘Name’ text field: the name of the newly created sample. It is prepopulated with the name of the directory. | * ‘Name’ text field: the name of the newly created sample. It is prepopulated with the name of the directory. | ||
* ‘Description’ text area: providing a number of description entries for the sample. It is prepopulated with common entries, including ‘Coordinate of the person’ and ‘Exposed physical dose’. You can add or remove any description entry. | * ‘Description’ text area: providing a number of description entries for the sample. It is prepopulated with common entries, including ‘Coordinate of the person’ and ‘Exposed physical dose’. You can add or remove any description entry. | ||
* ‘Apply to all’ checkbox: If checked, the current content in the ‘Description’ text area will be applied to all samples; in other words, all samples will have the same descriptions. | * ‘Apply to all’ checkbox: If checked, the current content in the ‘Description’ text area will be applied to all samples; in other words, all samples will have the same descriptions. | ||
* ‘Metaphase images included’ list: It is automatically populated with the names of all *.tif images in the directory and the image count. | * ‘Metaphase images included’ list: It is automatically populated with the names of all *.tif images in the directory and the image count. | ||
+ | |||
You can select another directory in the drop-down list, then the ‘Name’ text field, ‘Description’ text area and ‘Metaphase images included’ list will be updated accordingly. After you finish editing ‘Name’ or ‘Description’ for one sample, its content will be automatically saved. You can also click the ‘Clear’ button to clear the contents in all of the components. Each sample must have a name, but may not have any description. | You can select another directory in the drop-down list, then the ‘Name’ text field, ‘Description’ text area and ‘Metaphase images included’ list will be updated accordingly. After you finish editing ‘Name’ or ‘Description’ for one sample, its content will be automatically saved. You can also click the ‘Clear’ button to clear the contents in all of the components. Each sample must have a name, but may not have any description. | ||
+ | |||
+ | Then select a destination directory into which the created samples will be put by clicking the ' | ||
+ | |||
+ | {{ file: | ||
+ | |||
+ | ===== Download metaphase images from an external computer ===== | ||
+ | |||
+ | <WRAP group> | ||
+ | <WRAP half column> | ||
+ | It is very likely that metaphase images are produced by microscope devices of a remote laboratory, thus initially stored on a remote computer of the laboratory. In this case, the images need to be first downloaded to the local computer that you are using, which can also be accomplished by the bottom area of the right panel. In the drop-down list in the right part of the panel, select the item ' | ||
+ | |||
+ | The following figure shows that after successfully connecting to the remote computer, its name will be filled into the drop-down list and selected. For privacy, the right tree will only show the contents in one directory on the remote computer, which is the ' | ||
+ | </ | ||
+ | <WRAP half column> | ||
+ | {{ file: | ||
+ | </ | ||
+ | </ | ||
+ | |||
+ | {{ file: | ||
+ | |||
+ | ===== Monitor progress ===== | ||
+ | |||
+ | After finishing entering these preparation information, | ||
+ | |||
+ | <WRAP group> | ||
+ | <WRAP half column> | ||
+ | In the top grouping box of this progress dialog, the progress bar displays the percentage progress of creating the sample currently being selected in the drop-down list. The components n the middle grouping box display the following information: | ||
+ | * ‘Completed samples’ label: displays the number of samples that have finished creating to date / the total number of samples. | ||
+ | * ‘Elapsed time’ label: displays how long this sample creation process has been running for. | ||
+ | * Progress bar: displays the overall percentage progress of creating all samples. | ||
+ | |||
+ | The text area displays real-time feedback messages during the creation process, and will show a summary message after the process terminates. | ||
+ | |||
+ | You can also cancel the creation process by clicking the ‘Cancel’ button. Then an inquiry dialog will pop up to ask whether you want to keep the already created samples; if you click the ‘No’ button, these completed samples will also be deleted from the BGQ server, apart from terminating the creation process of the remaining samples. | ||
+ | </ | ||
+ | <WRAP half column> | ||
+ | {{ file: | ||
+ | </ | ||
+ | </ | ||