Open Microscopy Environment

Is there a way to generate a thumbnail directly from the ROI editor?

Our process now is to:
1. Open an image
2. Create an ROI
3. Generate an image from the ROI
4. Open that new image
5. Download it as jpg

It would be a huge time savings to create a thumbnail right in step 2.

Just a couple of clarifications...

I'm assuming that you are working only in Insight and that you're only creating Rectangular ROIs?
Do all your ROIs have a single shape (not multi-Z or multi-T)?
You want a download option in Insight that would download all the Rectangle ROI regions as individual images?

Cheers,

Will.

Sorry it took so long for me to get back to you.

Yes, we are using single shape, rectangles only ( 3000x300 ). We'd like to create a JPG from the ROI editor if possible. Now we create an image from an ROI (web client), open that new image up (in Insight) and create a thumbnail. It would be fantastic to do it one step.

Hi,

First, I'm just wondering how you are creating an image from ROI? Are you using the "Images_From_ROIs" script? If so, then you can do this in Insight without having to switch to the webclient. Or, you can also download the new image as a JPEG in webclient (don't have to use Insight).
Let me know if you need help with either of these.

Insight doesn't currently allow you to download an ROI region as a JPEG, although we'll certainly add this to our feature requests.

One option is to create a script similar to "Batch Image Export" that uses ROIs to export the region instead of the whole image. Again, this doesn't exist yet but shouldn't be too hard to tweak it. Let me know if this would be useful.

A possible workflow that is available to you right now, is to use the "render_image_region" url directly from the web.
If you know the x, y, width & height coordinates of your rectangle, you can combine this with imageId, z & t index to access a jpeg for that region of the form:

Code: Select all

/webgateway/render_image_region/<imageId>/<z>/<t>/?region=x,y,width,height

# for example, for imageId 8410, z=0, t=0, a 3000 x 300 region at x=2000, y=2000 go to:
/webgateway/render_image_region/8410/0/0/?region=2000,2000,3000,300


Then you can simply use your browser to "Save Image As..."

Having just looked at Insight, I see that the x,y,width & height are not displayed. Only width and height are shown (as pixels) under "Inspector" tab.
However, if you view the ROI in web, you can get these values from a tool-tip on the rectangle itself.
(see screenshot). This screenshot also shows that if you use these values in the render_image_region url then you'll get a jpeg of that region to download.

This is a bit hacky, and I'm not sure if it's any better than your current workflow (it saves you creating a new image) but I hope it helps.
I'll create tickets for 'download ROI region' and display of x,y,width and hight in Insight.

Regards,

Will.

Hi,
Just reading your post again, I'm not sure whether you really just want to download a thumbnail (E.g. 96 x 96 pixels) or if you want the full region?

I know that your title is "Thumbnails directly from ROI" but your workflow seemed to suggest download the new image as a jpeg:

Our process now is to:
1. Open an image
2. Create an ROI
3. Generate an image from the ROI
4. Open that new image
5. Download it as jpg

Thanks, will. This is very helpful.

I'm sorry I'm being so confusing. What we ultimately want is to create a JPEG of an ROI. In order to do this we are creating an image from an ROI and then doing a thumbnail of the image. If we could skip the "create an image from the ROI" step that would be nice. Thanks for submitting the ticket.


BTW, our image from ROI is 3000x3000 but our JPEG (thumbnail) is 96x96.

Hi,

I'm still a bit confused about why you care about thumbnails. Why do you want to generate a 96 x 96 image?
Does the workflow I outlined above get you what you need for now?
Cheers,

Will.