Category Archives: DICOM Search

DICOM Search – improved DICOM view (preview)

In the latest iteration of DICOM Search, we can now display your search results in a patient/study/series listing this way:

  • thumbnails are now displayed in the patient/study/series listing

This allows you to easily view the image without having to open it in the main viewing area.

  • you can filter on multiple values

In the above example, DICOM Search will display the images belonging to any patient/study/series containing the word brain OR rubo.

  • similarly, you can also filter on multiple values on the tag values

In the above example, only tags containing the word patient or physi are displayed.

You can now also display multiple images in the DICOM viewer.  You can adjust the position and size of each image panel to your requirements.  For e.g. if you are displaying 3 images, this could be one layout:

or you could lay them out this way:

You can open as many image panels as you require, limited primarily by the size of your display.

When you open multiple image panels, the DICOM details are also displayed for each image.  In the above example. the patient information would be displayed this way:

Similarly, the DICOM tag values found in each of the image are displayed this way:

If you apply a search filter, then only the tags matching the filter are displayed for all the images.

In the image viewer, there is now a magnification layer option.  Say you opened the following image:

You now have the option to magnify a part of the image, and also choose the magnification level and magnification area.

We hope to release DICOM Search early next month.  If you would like to have early access to the product and give it a try, please drop us a line at support@yohz.com.  We welcome any feedback you may have.

DICOM Search walk-through (preview)

We’ll do a walk-through on how to index your DICOM files and how to retrieve and display the images you need.

We start by first creating a library in DICOM Search, and selecting the Add/update images from folders option.

We then enter the file search pattern which will be used to locate our DICOM files.  Here, we’ll create thumbnails of our files, and enter the database file name to store the tag values and thumbnails in.

DICOM Search will then start processing the files and report the status as it goes along.

Once done, we can now run queries on the database.  In this example, we want to retrieve all MRI images where the study description contains the word head or torso.

At this point, you must be wondering how are we to remember the group and element values for each of the tags we want to search on.  You don’t have to remember those values.  Pressing F2 will bring up a tags window where you can search for any tag values by description.

E.g. if we search for modal, we can see all the tag values for modality.

Likewise, if we search for study, we can see the tags containing the word study.

When we run our query, all images matching our search criteria are returned.

Depending on our query, we may choose to return only the tag values we are interested in seeing, or in our example. all of the tag values because we entered

SELECT * …

DICOM Search offers an alternative view to display the images returned by your query.  This is the DICOM results viewer.

On the left, the query results are grouped by patient, study, series, and and related images.

You can display any of the image file in the main area simply by selecting it here.  DICOM Search will display the frames of the images at the top, and the selected frame in the main area.  You can play the sequence of images, display a single frame, view the transition from one frame to another and more in this area.

On the right, the values of the DiCOM tags are listed.  There is a patient specific tab that displays the patient data together with some image context tags

and a Tags tab that displays all the tag values found in the image.

If you have any suggestions on how we can improve on this new view, please do drop us a line at support@yohz.com.  Thank you.

See also:

DICOM Search – querying the database (preview 2)

Once DICOM Search has indexed the DICOM tags in your images, you can run queries against the tags table.  Selecting everything from the tags table, while possible, isn’t very useful and is very slow.

The reason is because there are over 2800 fields, and DICOM Search will struggle to maintain and display that many columns.  Thus, it is recommended that you select only the fields you are interested in.

You can quickly see which fields are available in your database by pressing F2 when in the SQL editor to bring up the Tags and Fields window.

Clicking on any of the tag values will add that value to the SQL editor area, so you do not need to manually enter the tag name.  In addition to the DICOM tags, there are also additional fields that DICOM Search populates in the tags table, as listed in the Field names tab.

In addition to your key fields, the other fields are used by DICOM Search to maintain a record of the processed images.  For the users, the useful fields are ds_thumbnail and ds_filenameds_thumbnail stores a thumbnail of the image and ds_filename stores the location of the image file when exported from your database, or when processed from your folder.

If the listed file name is present on your computer, you can open the image file in your DICOM viewer by double-clicking on the file name in DICOM Search.

Please see this post on how to index and extract images from your database to your computer using DICOM Search, and also how to add thumbnails to the tags database.

 

SQL syntax

The tag values are stored in a SQLite database, so you will use the SQLite SQL syntax to query the database.  In our example, our key fields are patientID and studyID, so we will always select those columns in case we want to query the source database.  We also select the ds_thumbnail and ds_filename columns to view the image thumbnail, and also have a link to the actual image.

Here are some examples of the types of queries you can run:

  • searching text values
    E.g. the Patient Name (tag group and element 0010,0010):SELECT patientID, studyID, ds_thumbnail, ds_filename FROM tags WHERE [00100010] = ‘Rubo’
  • searching for part of a text value
    E.g. to return all images where the patient name starts with Rubo:SELECT patientID, studyID, ds_thumbnail, ds_filename FROM tags WHERE [00100010] LIKE ‘Rubo%’E.g. to return all images where the patient name contains the word Rubo:SELECT patientID, studyID, ds_thumbnail, ds_filename FROM tags WHERE [00100010] LIKE ‘%Rubo%’

    E.g. to retrieve all images there the patient name ends with Rubo:

    SELECT patientID, studyID, ds_thumbnail, ds_filename FROM tags WHERE [00100010] LIKE ‘%Rubo’

  • searching date values
    E.g. the Study Date tag (tag group and element 0008,0020) for all studies made between Jan 1 1993 and Jan 1 1994:SELECT patientID, studyID, ds_thumbnail, ds_filename, [00080020] FROM tags WHERE [00080020] >= ‘1993-01-01’ AND [00080020] < ‘1994-01-01’Key point is you need to always enter the value you want to search for using yyyy-mm-dd format (year-month-date)
  • searching time values
    E.g. the Study Time tag (tag group and element 0008,0030), for all studies made between 1 PM and 2 PM.SELECT patientID, studyID, ds_thumbnail, ds_filename, [00080030] FROM tags WHERE [00080030] >= ’13:00′ AND [00080030] < ’14:00′Key point is you need to always enter the value you want to search for using hh:mm:ss format (hour:minutes:seconds).
  • searching numbers
    You can use all the usual equality and comparison symbols for numbers e.g. =, >, >=, <, <=E.g. the Intervention Drug Dose tag (tag group and element 0018,0028), where the value is greater than 25SELECT patientID, studyID, ds_thumbnail, ds_filename, [00180028] FROM tags WHERE [00180028] > 25

You can combine multiple conditions using the AND and OR operators e.g.

SELECT patientID, studyID, ds_thumbnail, ds_filename, [00080030] FROM tags WHERE ([00080020] >= ‘1993-01-01’ AND [00080020] < ‘1994-01-01’ AND [00080030] >= ’13:00′ AND [00080030] < ’14:00′) OR ([00100010] = ‘Rubo’)

To sort the results, use the ORDER BY option, and specify the field to sort by e.g. to sort the results by patient name (tag group and element

SELECT patientID, studyID, ds_thumbnail, ds_filename, [00080030] FROM tags WHERE ([00080020] >= ‘1993-01-01’ AND [00080020] < ‘1994-01-01’) ORDER BY [00100010]

To sort in descending order, add the DESC option after the field name e.g.

SELECT patientID, studyID, ds_thumbnail, ds_filename, [00080030] FROM tags WHERE ([00080020] >= ‘1993-01-01’ AND [00080020] < ‘1994-01-01’) ORDER BY [00100010] DESC

To limit the number of rows returned, use the LIMIT option.  For e.g. to retrieve the first 30 rows where the Intervention Drug Dose value is greater than 25, sorted by that field in descending order

SELECT patientID, studyID, ds_thumbnail, ds_filename, [00180028] FROM tags WHERE [00180028] > 25 ORDER BY [00180028] DESC LIMIT 30

See also:

DICOM Search – libraries (preview 1)

In DICOM Search, your DICOM images are organized into libraries.

You can populate each library with images from one or more databases, or from files on your computer.

Retrieving and indexing images from a database

DICOM Search can connect to PostgreSQL, SQL Server, Oracle, MariaDB, MySQL, and most popular database engines.  First, enter your connection details to connect to the database you want to process images from.

Enter the query to retrieve your images, together with the key fields used to uniquely identify the image.

You will then need to let DICOM Search know which are the key fields.

In our example, the patientID and studyID are the key fields.  Note that the key fields are for your own reference – when you query the tags database, the key fields are your link to the records in your source database.  When you want to extract the images or additional information from the source database, the key field values will help you in retrieving the relevant images.

DICOM Search will extract all the standard DICOM tag values and store them in a SQLite database.  You specify the name of this database file in the Tags database file name.

Indexing images from files on your computer

You can also index DICOM images if they are stored as files on your computer.   Enter the file paths and file search patterns to locate your DICOM files.  You can enter multiple values to search in.

 

Thumbnails

By default, only DICOM tag values are stored in the database e.g.

You can have DICOM Search create thumbnails for each of the image you process from your database or folder.

To create a thumbnail, select the Create thumbnail images option and enter the size of the thumbnail to create.

Once the thumbnails have been created, they will be displayed in a column named ds_thumbnail and can be displayed in DICOM Search together with the image tag values.

Exporting the images from your database

DICOM Search also helps you export your DICOM images from your database and store it in a folder on your computer.  To export the images, select the Extract images to folder option.

DICOM Search will then extract the images and store the file name in the ds_filename column.  When you run queries against the tags database and select this column, it will be highlighted in blue if the image file exists.  To open the file using your registered DICOM viewer, double click on the file name.

 

See also:

Cooking in the labs – a DICOM tags search application

This started out as a request from a user, and we thought it would be an interesting project for us.  We’re currently in the early stages of evaluating the feasibility of developing a DICOM tags search application.  The objective is to allow users to use SQL queries to search for DICOM images using values from the DICOM tags embedded in the images.

Step 1 – reading the tags from your DICOM images

We plan to allow you to read the DICOM images from a database, or from DICOM files already on your computer.

Step 2 – storing the data elements/tag values

This is the hardest part.  A DICOM image can contain both standard and private data elements/tags.  For a start, we will only be indexing most of the standard data elements/tags (over 2800).

Step 3 – querying the tag values

Once stored in a database, users can use SQL syntax to query the tag values.  We will also look into adding a query builder to help non-technical users.

Step 4 – displaying the images

Once we have the results of the query, we can display the images using the user’s preferred DICOM viewer.

Issues/bottlenecks

We do not have any experience working with PACS nor have access to any such system.  We are approaching this purely from a database developer perspective – read the images, store the tag values in a database, allow users to query the database, and display the results.

If you are interested in such an application and can spare some time to help us test the application as we go along, or there are features you would like to see in such an application, please drop us an email at support@yohz.com.  Thank you.

See also: