Image Analysis ROI to Tile Region

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David Bulmer
Posts: 2
Joined: Mon May 16, 2022 5:17 pm

Image Analysis ROI to Tile Region

Post by David Bulmer »

Is it possible to transfer regions detected by the analysis pipeline to new tile regions. I have done similar things using the guided acquisition macros, but i would like to have the option to manually do something similar on a sample by sample basis by copying the ROIs from the analysis of an image and have the new polygon tile regions created.
Any help greatfully received
David
(Zen 3.1 on Cell Discoverer 7)
CarlZeissMicroscopy3
Posts: 180
Joined: Wed May 20, 2020 10:10 am

Re: Image Analysis ROI to Tile Region

Post by CarlZeissMicroscopy3 »

Hello David Bulmer,

I'm not sure if I fully understood what you intend to do but here are two code snippets that hopefully point into the 'right' direction.

From Analysis result in an image to the regions of a class and finally to the polygon:

Code: Select all

zenRegions = Zen.Analyzing.GetRegions(imageWithIasResult, "className")
zenRegion = zenRegions[0]

pointsPolygon = zenRegion.GetPolygon()
pointsPolygon = zenRegion.GetPolygonHighDetails()

X = pointsPolygon[0].X
Y = pointsPolygon[0].Y
Adding a polygon to an experiment:

Code: Select all

listZenPoints = []
x = 120.0
y = 40.0
pt = ZenPoint(x, y)
listZenPoints.append(pt)
x += 200.0
pt = ZenPoint(x, y)
listZenPoints.append(pt)
y += 200.0
pt = ZenPoint(x, y)
listZenPoints.append(pt)

experiment.AddPolygonExperimentRegion(zenScaling, stagePositionLeftTop, blockIndex, listZenPoints, Colors.AliceBlue, False, False, False)
The code is not intended to run 'as is' and is also not 'tested'!

Please come back on me if this is not of use for you.
David Bulmer
Posts: 2
Joined: Mon May 16, 2022 5:17 pm

Re: Image Analysis ROI to Tile Region

Post by David Bulmer »

Hi
I will look into these code suggestions, though my knowledge of the Zen Macro system is limited at best.
The idea is to create a macro which can be added to the toolbar in Zen which can take a presaved and analysed image and transpose the ROI's into new polygon tile regions which can be reimaged at different settings. Essentially the way the Guided Acquisition macro works, but on a more manual basis, where instead of doing Image1/Analysis/Image2 sequentially, Image2 can be acquired with just the Analysed Image. This will allow users to either analyse all of the prescans offline using the Analysis module on a second PC, or annotate the regions of interest at their leisure, save the analysis or graphics into the original czi, then open that czi at a later date on the microscope pc and have the macro transcribe the ROIs into new tile regions. From there they would just need to set z and run rather than having to draw the tile regions all manually.
As a second goal, it would be nice to be able to draw a tile region, and have the ability to image random fields within the tile region limits in a similar way to stereology softwares)
Any help greatfully received
David
frederick harley
Posts: 2
Joined: Sat May 21, 2022 9:12 am

Re: Image Analysis ROI to Tile Region

Post by frederick harley »

Thanks, @carl! I want to export tiles from within an ROI (in this case the area of infarct) so I can run images through a macro for particle analysis in ImageJ.

However, we want to maintain a consistent tile size (if possible!).
Also, to ensure flexibility across studies, we would like to be able to export at various magnifications if possible.
we need the individual images to be exported so we can overlay the particle analysis outlines over the original image to manually check the results after.
CarlZeissMicroscopy3
Posts: 180
Joined: Wed May 20, 2020 10:10 am

Re: Image Analysis ROI to Tile Region

Post by CarlZeissMicroscopy3 »

Hello frederick harley,
  • open the image in Zen blue
  • draw the ROI via Menu / Graphics / "Draw region of interest"
  • Right mouse click on the ROI brings up a Menu, select "Create Subset image from ROI"
  • When the new image (just showing the ROI) is active select Menu / File / "Export/Import" / Export
  • Select 'Show All' in the title of the window to obtain all export features (e.g. activate Original data, Tiles / "Export Selected Tiles", etc.)
I hope this helps.
Daxton Tate
Posts: 1
Joined: Mon Jan 16, 2023 3:55 pm

Re: Image Analysis ROI to Tile Region

Post by Daxton Tate »

David Bulmer wrote: Mon May 16, 2022 5:24 pm Is it possible to transfer regions detected by the analysis pipeline to new tile regions. I have done similar things using the guided acquisition macros, but i would like to have the option to manually do something similar on a sample by sample basis by copying the ROIs from the analysis of an image and have the new polygon tile regions created.
Any help greatfully received from https://knifeplatoon.com
David
(Zen 3.1 on Cell Discoverer 7)
Hey, a quick question: How does a microarray measure gene expression? Thanks
Jameson Silas
Posts: 1
Joined: Wed May 03, 2023 10:24 pm

Re: Image Analysis ROI to Tile Region

Post by Jameson Silas »

David Bulmer wrote: Mon May 16, 2022 5:24 pm Is it possible to transfer regions detected by the analysis pipeline to new tile regions. I have done similar things using the guided acquisition macros, but i would like to have the option to manually do something similar on a sample by sample basis by copying the ROIs from the analysis of an image and have the new acacia material polygon tile regions created.
Any help greatfully received
David
(Zen 3.1 on Cell Discoverer 7)
Yes, it is possible to transfer regions detected by the analysis pipeline to new tile regions in image analysis software that supports region copying and pasting.
Cody Walls
Posts: 4
Joined: Fri May 05, 2023 2:25 pm

Re: Image Analysis ROI to Tile Region

Post by Cody Walls »

David Bulmer wrote: Mon May 16, 2022 5:24 pm Is it possible to transfer regions detected by the analysis pipeline to new tile regions. I have done similar things using the guided acquisition macros, but i would like to have the option to manually do something similar on a sample by sample basis by copying the ROIs from the analysis of an image and have the new polygon tile regions created.
Any help greatfully receivedhappy wheels game
David
(Zen 3.1 on Cell Discoverer 7)
You must export the individual photographs so that we may overlay the particle analysis outlines over the original image and manually check the results.
helen dam
Posts: 3
Joined: Tue May 30, 2023 10:33 am

Re: Image Analysis ROI to Tile Region

Post by helen dam »

David Bulmer wrote: Wed May 18, 2022 3:19 pm Hi
I will look into these code suggestions, though my knowledge of the Zen Macro system is limited at best.
The idea is to create a macro which can be added to the toolbar in Zen which can take a presaved and analysed image and transpose the ROI's into new polygon tile regions which can be reimaged at different settings. Essentially the way the Guided Acquisition macro works, but on a more manual basis, where instead of doing Image1/Analysis/Image2 sequentially, Image2 can be acquired with just the Analysed Image. This will allow users to either analyse all of the prescans offline using the Analysis module on a second PC, or annotate the regions of interest at their leisure, save the analysis or graphics into the original czi, then open that czi at a later date on the microscope pc and have the macro transcribe the ROIs into new only up tile regions. From there they would just need to set z and run rather than having to draw the tile regions all manually.
As a second goal, it would be nice to be able to draw a tile region, and have the ability to image random fields within the tile region limits in a similar way to stereology softwares)
Any help greatfully received
David
yes, i think so
Last edited by helen dam on Mon Sep 25, 2023 9:43 am, edited 1 time in total.
Weinbergerson burnan
Posts: 1
Joined: Mon Jul 17, 2023 5:37 pm

Re: Image Analysis ROI to Tile Region

Post by Weinbergerson burnan »

Yes, it is generally possible to transfer regions detected by an analysis pipeline to new tile regions. While the specific steps may vary depending on the software or tool you are using for image analysis the general approach involves the following:

Identify and extract the regions of interest (ROIs) detected by the analysis pipeline in the original image.
Copy or export the ROIs as polygonal or boundary data.Create new tile regions or define the desired sampling areas in the new image or sample.Import or paste the ROIs from the original image into the new tile regions, aligning them appropriately for more info https://cryptopostage.info/
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