Navigation question

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Mariam Melkumyan
Posts: 1
Joined: Fri Mar 19, 2021 2:22 am

Navigation question

Post by Mariam Melkumyan »

Hello. I am trying to figure out whether there is a way to navigate from a 20x or a 40x image to a big tiled image. I am imaging the central amygdala at 20x and I need to be able to verify that I am in the correct region. I know I can use tiles to take a whole brain image and then use more tiles to zoom in to the correct region but I am not able to save the ROI lines on the newly acquired image for some reason. I would like to do 2 thing: save the ROI that I mark on the tiled preview image on the acquired ROI image, and be able to show where the zoomed in ROI image is on the big tiled image postimaging.

I have used a camera based Keyence microscope before and on that microscope if you take a 4x image of the whole brain slice and a 40x image of the desired location, you can then go back and tell the program to mark on the 4x image where the 40x image was taken from. I would love to be able to do that on Zen.
CarlZeissMicroscopy3
Posts: 180
Joined: Wed May 20, 2020 10:10 am

Re: Navigation question

Post by CarlZeissMicroscopy3 »

Hello Mariam Melkumyan,

this is a forum primarily for Open Application Development (OAD)!
save the ROI that I mark
In the Menu choose 'Graphics' and then 'Draw Region of Interest'.
You can now draw the ROI in your (tiled) image. Make a right mouse click on the ROI and select 'Create Subset Images from ROI'.
Now a 'new image' is generated that corresponds to the ROI and you just have to save it.
show where the zoomed in ROI image is on the big tiled image
Via OAD it is possible to convert the ROI into a Rectagle so that the Rectangle is saved with the overview image.

I hope this helps.
julie diane
Posts: 24
Joined: Wed Jun 28, 2023 1:25 am

Re: Navigation question

Post by julie diane »

Mariam Melkumyan wrote: Fri Mar 19, 2021 2:27 am Hello. I am trying to figure out whether there is a way to navigate from a 20x or a 40x image to a big tiled image. I am imaging the central amygdala at 20x and I need to be able to verify that I am in the correct region. I know I can use tiles to take a whole brain image and then use more tiles to zoom in to the correct region but I am not able to save the ROI lines on the newly acquired image for some reason. I would like to do 2 thing: save the ROI that I mark on the tiled preview image on the acquired ROI image, and be able to show where the zoomed in ROI image is on the big tiled image postimaging.

I have used a camera based Keyence microscope before and on that microscope if you take a 4x image of the whole brain slice and a 40x image of the desired location of Calculate percentage from CGPA, you can then go back and tell the program to mark on the 4x image where the 40x image was taken from. I would love to be able to do that on Zen.
It sounds like you are working with imaging and microscopy using the Zen software. While I don't have access to your specific microscope or software setup, I can provide some general guidance based on your description.

Saving ROI on Tiled Preview Image: If you are unable to save the ROI lines on the newly acquired image for some reason, there may be a configuration or settings issue within the Zen software. Check the settings related to image acquisition and saving ROIs to ensure everything is configured correctly. If you encounter specific issues, reaching out to the Zen software's support team or community forums might provide you with more tailored assistance.

Linking Zoomed-in ROI Image to Big Tiled Image: In Zen software or similar microscopy imaging software, there is often a feature to overlay or link images taken at different magnifications. This feature allows you to see the specific region of interest (ROI) from the zoomed-in image on the larger tiled image. To achieve this, you would need to mark the ROI on the zoomed-in image and then link or overlay that ROI on the big tiled image. This way, you can easily identify the location of the zoomed-in ROI within the larger image.

To accomplish this, refer to the Zen software's documentation or support resources for instructions on how to link or overlay images. The process may vary depending on the version and configuration of the software you are using.

If you are unable to find the specific features you need in Zen or encounter any difficulties, consider consulting the user manual or contacting the software's support team for more guidance.

Remember that the exact steps and capabilities may vary depending on the microscope model and the version of the software you are using. Always refer to the manufacturer's documentation and support resources for the most accurate and up-to-date information.
julie diane
Posts: 24
Joined: Wed Jun 28, 2023 1:25 am

Re: Navigation question

Post by julie diane »

Mariam Melkumyan wrote: Fri Mar 19, 2021 2:27 am Hello. I am trying to figure out whether there is a way to navigate from a 20x or a 40x image to a big tiled image. I am imaging the central amygdala at 20x and I need to be able to verify that I am in the correct region. I know I can use tiles to take a whole brain image and then use more tiles to zoom in to the correct region but I am not able to save the ROI lines on the newly acquired image for some reason. I would like to do 2 thing: save the ROI that I mark on the tiled preview image on the acquired ROI image, and be able to show where the zoomed in ROI image is on the big tiled image postimaging.

I have used a camera based Keyence microscope before and on that microscope if you take a 4x image of the whole brain slice and a 40x image of the desired location of dirt bike accesories, you can then go back and tell the program to mark on the 4x image where the 40x image was taken from. I would love to be able to do that on Zen.
Image Acquisition with Marking ROIs:

a. Start by acquiring your 20x or 40x images as needed.

b. Open the acquired images in Zen software.

c. To mark ROIs, you can use the "Annotation" or "Overlay" tools within Zen. These tools allow you to draw shapes, lines, and text directly on your images.

d. Once you've marked the ROIs on your images, save the images with the annotations. This will ensure that the ROIs are saved along with the images.

Navigation and Comparison:

a. If you want to compare a zoomed-in ROI image with a larger, tiled image, you can use Zen's image navigation tools.

b. Open both the zoomed-in ROI image and the larger, tiled image in Zen.

c. Use the navigation tools to move and align the zoomed-in ROI image with the corresponding location on the larger, tiled image. Zen typically provides features like panning, zooming, and scrolling to help you navigate and align the images accurately.

d. You can visually compare the two images to verify that you're in the correct region.

Saving Annotations and Navigation State:

a. To save the marked ROIs and navigation state (i.e., the position and zoom level of the images), you can usually save your Zen workspace or project. This will allow you to revisit and continue your work later while retaining all annotations and image positions.

b. The specific steps for saving workspace or project files may vary slightly depending on the version of Zen you're using, so it's a good idea to consult the Zen software user manual or help resources for detailed instructions.

By following these steps, you should be able to mark ROIs on your images, navigate between images, and save both the marked ROIs and the navigation state in Zen software. If you encounter any difficulties or if your specific version of Zen has unique features or workflows, I recommend reaching out to Zeiss support or consulting the user manual for your version of Zen for further guidance.
Xdas Dasbeer
Posts: 1
Joined: Fri Sep 22, 2023 12:43 pm

Re: Navigation question

Post by Xdas Dasbeer »

Hello! It sounds like you're dealing with some image navigation and annotation challenges in Zen software. While I'm not familiar with the specific features of Zen.
fnaf breach
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Joined: Thu Oct 19, 2023 11:47 am

Re: Navigation question

Post by fnaf breach »

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Maria Linda
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Re: Navigation question

Post by Maria Linda »

It seems like Zen is giving you a run for your money when it comes to picture navigation and annotation. Although I am not well-versed in Zen's defining characteristics.
Rufus Whiliam
Posts: 1
Joined: Mon Mar 04, 2024 7:49 pm

Re: Navigation question

Post by Rufus Whiliam »

Navigating from a 20x or 40x image to a tiled view is essential for precise region identification. In Zen, the ability to save ROI lines on acquired images and indicate the zoomed-in ROI's location facilitates efficient post-imaging analysis. Cleaning up the interface for smoother operation would enhance user experience.
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