how_to_use_the_dicomizer_tool_for_anonymisation
Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision Next revision | Previous revision | ||
|
how_to_use_the_dicomizer_tool_for_anonymisation [2023/02/15 14:53] yves |
how_to_use_the_dicomizer_tool_for_anonymisation [2023/11/09 17:31] (current) chris |
||
|---|---|---|---|
| Line 1: | Line 1: | ||
| - | ===== DICOMizer tool instructions ===== | + | ====== DICOMizer Tool Instructions ====== |
| This guide explains step by step what you need to do to convert any type of whole slide image in a DICOM format and remove all identifiable data. | This guide explains step by step what you need to do to convert any type of whole slide image in a DICOM format and remove all identifiable data. | ||
| Line 5: | Line 5: | ||
| ==== PMA.start ==== | ==== PMA.start ==== | ||
| - | You need to have PMA.start and the DICOMizer software installed on your pc. Look for these logo’s: | + | You need to have PMA.start and the DICOMizer software installed on your pc. Look for these logos: |
| {{::dicomizer_1.png?200|}} | {{::dicomizer_1.png?200|}} | ||
| Line 14: | Line 14: | ||
| {{:dicomizer_2.png?400|}} | {{:dicomizer_2.png?400|}} | ||
| - | ==== Locating the tool ==== | + | ==== Using the DICOMizer Tool ==== |
| - | The DICOMizer software runs as a command prompt. You will need to type a ‘Dicomize’ command. There are 3 important lines of text to type: | + | The DICOMizer software runs as a command prompt. You will need to type a ‘Dicomize’ command. There are 3 important lines of text to type which this page will guide you through: |
| - | - the location of the DICOMizer software | + | - The location of the DICOMizer software |
| - | - the location of the file you want to convert | + | - The location of the file you want to convert |
| - | - where you want the resulting image to be stored. | + | - The location you want the final DICOMized image to be saved. |
| - | To establish the location of the DICOMizer tool on your pc: right-mouse click on the DICOMizer icon, then click properties, in the properties popup window, you can copy the target file with a right mouse click and then copy it. | + | |
| + | **1. Program Location**\\ To establish the location of the DICOMizer tool on your pc: right-mouse click on the DICOMizer icon, then click properties, in the properties popup window you can copy the target file path with a right mouse click and then copy it. | ||
| {{:dicomizer_3.png?200|}} {{ :dicomizer_4.png?400|}} | {{:dicomizer_3.png?200|}} {{ :dicomizer_4.png?400|}} | ||
| - | Paste the program file link in a text file for future use, it should look similar to this example: //c:\Users\RudyHovelinckPathoma\AppData\Local\Programs\Pathomation\Dicomizer\Dicomizer.exe// | + | Paste the program file path in a text file for future use. It should look similar to this example: //c:\Users\RudyHovelinckPathoma\AppData\Local\Programs\Pathomation\Dicomizer\Dicomizer.exe// |
| + | **2. Source Image Location**\\ | ||
| Next you need to know the location path of the images you want to DICOMize. Open the folder on your local disk drive where your slides are located. This is a good moment create a folder where you want the DICOMized images to be stored. | Next you need to know the location path of the images you want to DICOMize. Open the folder on your local disk drive where your slides are located. This is a good moment create a folder where you want the DICOMized images to be stored. | ||
| - | |||
| - | ==== DICOM conversion ==== | ||
| - | In the example below we will describe how to DICOMize the image ‘TIN1’ and store the DICOMized image in the folder ‘Dicom’ | + | In the example below we will describe how to DICOMize the image ‘TIN1’ and store the DICOMized image in the folder ‘Dicomized slides’ |
| {{::dicomizer_5.png?600|}} | {{::dicomizer_5.png?600|}} | ||
| - | Next open ‘TIN1’ (1) in the PMA.start viewer, you can see the location of the image to be DICOMized in (2), select the path text and copy it (eg Ctrl-C). Paste the image file link in a text file for future use, it should look similar to this example: | + | Next open ‘TIN1’ (1) in the PMA.start viewer, you can see the location of the image to be DICOMized in (2), select the path text and copy it (Ctrl-C or right click -> copy). Paste the image file path in a text file for future use. It should look similar to this example: |
| //c:\Users\RudyHovelinckPathoma\OneDrive - Pathomation\03 Pathomation\SLIdes\TIN 1.svs// | //c:\Users\RudyHovelinckPathoma\OneDrive - Pathomation\03 Pathomation\SLIdes\TIN 1.svs// | ||
| {{::dicomizer_6.png?600|}} | {{::dicomizer_6.png?600|}} | ||
| - | Next open the folder where you want the resulting DICOMized images to be stored, you can see the location of the folder by selecting the folder header text and copying it with a right mouse click and the copy function in the menu. Paste the image file link in a text file for future use, it should look similar to this example: | + | **3. The Output Location** \\ Next open the folder where you want the resulting DICOMized images to be saved. You can see the location of the folder by selecting the folder header text and copying it (Ctrl+C or right click -> copy). Paste the image file path in a text file for future use. It should look similar to this example: C:\Users\RudyHovelinckPathoma\OneDrive - Pathomation\03 Pathomation\SLIdes\Dicomized slides |
| - | //C:\Users\RudyHovelinckPathoma\OneDrive - Pathomation\03 Pathomation\SLIdes\Dicomized slides// | + | |
| {{:dicomizer_7.png?600|}} | {{:dicomizer_7.png?600|}} | ||
| Line 58: | Line 57: | ||
| "C:\Users\RudyHovelinckPathoma\OneDrive - Pathomation\03 Pathomation\SLIdes\Dicomized slides"// | "C:\Users\RudyHovelinckPathoma\OneDrive - Pathomation\03 Pathomation\SLIdes\Dicomized slides"// | ||
| - | __It is very important to put the file location and destination between “ ” and have a space between the 3 text lines__ | + | _It is very important to put the file location and destination between “ ” and have a space between the 3 text lines._ \\ |
| - | You can add several images you want to DICOMize at once type one after the other, again do not forget to add “ before and after every file name. | + | You also can batch several images you want to DICOMize at once, insert the input image file paths one after the other, again do not forget to add “ before and after every file name, and only include the destination path once at the end of the command like so: |
| + | |||
| + | //c:\Users\RudyHovelinckPathoma\AppData\Local\Programs\Pathomation\Dicomizer\Dicomizer.exe \\ | ||
| + | “c:\Users\RudyHovelinckPathoma\OneDrive - Pathomation\03 Pathomation\SLIdes\TIN 1.svs” \\ | ||
| + | “c:\Users\RudyHovelinckPathoma\OneDrive - Pathomation\03 Pathomation\SLIdes\TIN 2.svs”\\ | ||
| + | “c:\Users\RudyHovelinckPathoma\OneDrive - Pathomation\03 Pathomation\SLIdes\TIN 3.svs”\\ | ||
| + | “C:\Users\RudyHovelinckPathoma\OneDrive - Pathomation\03 Pathomation\SLIdes\Dicomized slides”//\\ | ||
| {{:dicomizer_10.png?600|}} | {{:dicomizer_10.png?600|}} | ||
| Line 67: | Line 73: | ||
| {{:dicomizer_11.png?600|}} | {{:dicomizer_11.png?600|}} | ||
| - | Now your DICOMized image is in the destination folder and all metadata has been removed. At this step you can also remove the label by deleting the file with extension ‘label’. | + | Now your DICOMized image(s) can be found in the destination folder with all metadata removed. |
| + | |||
| + | ==== Examining DICOM results ==== | ||
| {{:dicomizer_12.png?600|}} | {{:dicomizer_12.png?600|}} | ||
| - | You will notice that there seem to be multiple copies of the same file. This is due to the DICOM specifications, different zoom levels are captured in different slides. Click on any of these images to open the whole slide image. For uploading to My Pathomation you will also see multiple files, you can start the upload process from any of the files, all the information will be uploaded | + | You will notice that there seem to be multiple copies of the same file. This is due to DICOM specifications which require different zoom levels to be captured in different slides. Click on any of these images to open the whole slide image. When uploading to My Pathomation, you will also see multiple files, however you can start the upload process from any of the files and all of the magnification levels and information will be uploaded. |
| {{:dicomizer_13.png?600|}} | {{:dicomizer_13.png?600|}} | ||
| + | ==== Anonymization ==== | ||
| + | |||
| + | You can remove the label by deleting the file with extension ‘label’. | ||
| + | |||
| + | ==== Current limitations ==== | ||
| The DICOMizer doesn’t support fluorescent images, or z-stacks. | The DICOMizer doesn’t support fluorescent images, or z-stacks. | ||
how_to_use_the_dicomizer_tool_for_anonymisation.1676461981.txt.gz · Last modified: 2023/02/15 14:53 by yves
Page Tools
