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 processed sample page.
To create a new sample, click the icon. A dialog will appear to allow selection of a directory. Select the desired sample directory containing metaphase image files and click “Select Folder”.
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”.
ADCI supports metaphase images supplied in TIFF/TIF or JPEG/JPG format. All TIFF/TIF and JPEG/JPG images within the specified Sample directory will be examined while processing the sample in the process queue even if both formats are present in the same Sample. Files with other extensions present in the specified Sample directory are ignored by ADCI.
It is preferable to supply ADCI with TIFF/TIF images as it is a “lossless” image format, while JPEG/JPG is typically a “lossy” format. During the process of “lossy” compression, image fidelity is reduced which may lead to different dicentric counts between TIFF/TIF and JPEG/JPG formats even if the images were derived from the same microscope and saved in both TIFF/TIF and JPEG/JPG formats. While JPEG/JPG images may appear to have no perceptible decline in image fidelity, image processing algorithms used within ADCI are sensitive to minor changes in quality.
To import a sample which has previously been saved, click the icon. A dialog will appear allowing you to select saved samples from the file system. Saved samples have the file extension adcisample.
Samples cannot be saved until they are processed to become a processed sample. When a sample has completed processing a dialog appears asking if you would like the save the processed sample. To save a processed sample at a later time, highlight the appropriate sample in the Samples list within the main GUI and click the icon.
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 recoverable if multiple samples were processed in the process queue. For more information on recovering unsaved samples, consult the sample recovery page.
To edit the description of an existing sample, highlight the appropriate sample within the Sample list in the main GUI and click the 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.
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.
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 mainGUI under the heading “Processed”. Unprocessed samples must be added to the process queue for processing. To do so, highlight an unprocessed sample and click the 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 icon. All items currently in the process queue can be processed sequentially in one click by clicking the icon.
When a sample is highlighted in the Sample list within the main GUI, information about the highlighted sample is shown in the console. DC counts and frequencies will be part of this information if the sample has been processed.
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 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.