Meyer Navigator for ScanImage
Posted in Software
Software from Stephan Meyer Zum Alten (Gilbert lab, Rockefeller):
I put together a sort of Navigator for Janelia Farms ScanImage Two Photon control software, which we use a lot in our lab. There was no way in the existing version to visualize where you are, have been, distances, mark where you want to go back to (and move there automatically), etc. There are ROIs, but those are just numbers.
So this plots it all in a graph that you can also annotate. Might be useful for others too. It was made for the Sutter manipulator, I think it should also work with the others that ScanImage supports, but I haven’t tried it. Feel free to use it.
Sadly, the scanimage people never set up a Wiki/Forum or something like this for sharing SI addons, hardware drivers and userfunctions.
Shall we simply do this here?
…just to prevent this (http://goo.gl/yE8B7M) from happening over and over again?
😉
I could offer tons of semi-functional widgets, drivers etc.
I am certain that pretty much every SI lab developed their own userfunctions/addons/modifications… that’s one of the reasons SI is so popular.
cheers,
ybot
I second the sentiment. We need a ScanImage user repository. I to, have made a spatial navigator (in Igor Pro) that complements ScanImage. More generally, any directory of .tif files that have motor coordinates.
The documentation below is a work in progress but we are using the software in the lab every day.
Canvas:
http://www.robertcudmore.org/maptracker/v2/canvas/
mp285Canvas:
http://www.robertcudmore.org/maptracker/v2/mp285/
I was emailing with the ScanImage guys a while back and they said they plan to set up a user repository. So not sure where that is going.
It would be really nice to have all the user stuff around, like ImageJ has a database of plugins.
That thing in igor looks really nice. I thought of something like that also, that tiles together what you took.
I will check that out. Thanks
The download is now available here
http://digitalcommons.rockefeller.edu/gilbert_laboratory/1/
it also has the added option to inverse the axes to match your setup, as requested by Bill Bennett from University of Tasmania.
Just to add a public vote of thanks to Stefan for tweaking the code, and to add that his Navigator plugin works well with our Scientifica 2P system under ScanImage 3.8.1 (with the Scientifica MMBP baseplate)
We find it extremely useful for mapping arbors and ROIs in GFP cranial window mice, as I find it much easier to move quickly around a visual map than a list of coordinates stored as reference points.
Scientifica have developed something similar to go with their own LavView software, but I haven’t personally used it. There’s a demo video on the Scientifica website.