add an extract functionality

[katjaq]

Is this a feature request or a bug report?

an awesome new feature!

What is the current behavior?

Currently, MicroDraw loads and displays the data as is. Depending on the scan of the histological data, sometimes there is a large empty border around the actual data.

What is the expected or desired behaviour?

Would be nice if MicroDraw could allow the user to draw a rectangle around the field of view that they would like to keep, and then to copy everything inside that rectangle into a new file.

[xgui3783]

I will be happy to implement this. I have a version of this happening locally already.

[katjaq]

Waaaaaaa!! This is awesome! I was about to put more information into this issue and realised that had no clear idea of how this could work. I'd be super interested if you could take that!! :D 👍

There were a few thoughts form a quick brainstorm...

• The cropped data should be saved in DZI format
• Ideally be saved server side since it might be very big
• This might risk filling up our space very quickly... how could that be handled?
• How could the user then get the cropped data?

What do you think?

Looking forward to your solution and suggestions!! 👍 👍 👍

[xgui3783]

Hmm, the previous tool we made saved full res PNG. That has the advantage of being able to be opened anywhere without special programs. I can take a look at DZI images, but native support for DZI would be limited on MacOS/Windows/Linux (?) Alternatively, we may look at giving the user an option to download/save as DZI, 1x zoom, 2x zoom 3x zoom or full res PNG?

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On 15 Oct 2017 22:02, "katja heuer" ***@***.***> wrote: Waaaaaaa!! This is awesome! I was about to put more information into this issue and realised that had no clear idea of how this could work. I'd be super interested if you could take that!! :D 👍 There were a few thoughts form a quick brainstorm... - The cropped data should be saved in DZI format - Ideally be saved server side since it might be very big - This might risk filling up our space very quickly... how could that be handled? - How could the user then get the cropped data? What do you think? Looking forward to your solution and suggestions!! 👍 👍 👍 — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#81 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ASe-FyDkTC4UG1NoWoPJ7myh4COzWdUrks5ssmS3gaJpZM4P5sbF> .

[xgui3783]

re: brainstorm thoughts:

• png files (if they make it in) can be downloaded to the localdrives of the users. dzi files: would be nice if we could just save the metadata (crop area), instead of duplicating the data.
• dzi files: for sure. even if we are just saving the metadata (x,y, dx, dy, pointer to dzi), it makes sense to save the metadata serverside, since software such as microdraw is needed to view the dzi images (again, correct me if I am mistaken)
• user get cropped data: user could choose to save a copy of png on their local drive (as per previous comment). My understanding is, even if the user chose to save the selection as dzi, when they open the dzi, it (the cropped dzi) would be rendered in microdraw, where they could choose a crop again, and choose to save it as a png or dzi

Though the implementation of this metadata would most likely increase the complexity.