Working with merged images

[rachelprior]

How can I work with merged images? The software doesn't seem to be able to merge them itself, so I get a bunch of tiles separately. I can merge the images myself and just do a max project, but then I don't know how to calculate the voxel size for the dims file. Will it be the same size as the voxels in one of the tiles from that image? This is quite important as a lot of my images are merges, particularly for the live tracking!!

[rosscarter3]

If you can merge the stacks, then put them into lif2stack it might work... The voxel size will remain unchanged, unless the software you use to merge changes it, which it shouldn't....

I should be at JIC on Tuesday next week if you're around (and maybe Mike/Stan/Veronica) for a quick discussion

[rachelprior]

I think I've got a hack around it, thanks! Tuesday sounds good, it's the day before I go away for a while so might be good to touch base and explain what our plan of action is. I'll speak to Mike, not sure what Stan and Veronica are up to, they might still be away?

[binish-vglab]

Yes they will be away and will not available by email either. I'd also like to join in for a dummies version of the problems, I have no idea what your talking about sometimes but I know that I will be needing this information. Also, any luck with the segmentation of my images, Ross? Binish Sent from my Samsung Galaxy smartphone.

…

-------- Original message -------- From: rachelprior <notifications@github.com> Date: 14/06/2017 15:27 (GMT+00:00) To: rosscarter3/leaf_analysis_toolkit <leaf_analysis_toolkit@noreply.github.com> Cc: Subscribed <subscribed@noreply.github.com> Subject: Re: [rosscarter3/leaf_analysis_toolkit] Working with merged images (#5) I think I've got a hack around it, thanks! Tuesday sounds good, it's the day before I go away for a while so might be good to touch base and explain what our plan of action is. I'll speak to Mike, not sure what Stan and Veronica are up to, they might still be away? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#5 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AQmqy2m1RcMZiBIQMrNTG5Ib6fkHSTCLks5sD-2KgaJpZM4N57Mh>.

[rosscarter3]

Yes @binish-vglab that would be fine! I had a look at your images and I think the resolution might be to low and there's quite a lot of background noise, but we can have a go!

[rachelprior]

What time is good for you guys? Mike and I can do any time. FYI we have decided to manually seed all the images as the SPM stuff doesn't seem to be working well enough for us - unless you have any ideas for parameter fiddling? Seems to be oversegmenting large cells in the tip, and undersegmenting small cells in the base...