Registering brains

[Dr Gregory Jefferis]

Dear Adam,

On 16 Jul 2015, at 7:04, Adam Claridge-Chang wrote:

> I'm curious about how to register our own brains to a reference brain,
> is that something done in NAT, FIJI or VFB?

You can see bit.ly/flybrains for templates. FCWB is the template used
for FlyCircuit data, but I recommend JFRC2 if you have nc82 stained
brains.

For registration you can try https://github.com/jefferis/fiji-cmtk-gui
NB this only tested on a mac unfortunately. I recommend the Cachero 2010
registration parameters.

You can read much more about this in a CSH protocols articles that they
seem to have divided into 3

http://cshprotocols.cshlp.org/content/2013/4/pdb.prot071712.short

the staining and image registration ones are what you want. Note however
that the image registration GUI has been superseded by the one linked
above.

Best wishes,

Greg.

--
Gregory Jefferis, PhD
Division of Neurobiology
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge, CB2 OQH, UK

http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis
http://jefferislab.org
http://flybrain.stanford.edu

[Gregory Jefferis]

Sent from my iPad

> On 18 Jul 2015, at 08:55, Adam Claridge-Chang <ada...@gmail.com> wrote:
>
> One snag is that our nc82 attempts never worked, so we use DLG.

You can use the FCWB template.

> Marta mentioned there might be a bridging registration using double-stained DLG/nc82 brains?

There is a bridging reg but it's not perfect since it was not based on a double stained brain. However we have used it extensively.

> If not, or if you think the results won't be so good we will order some Chemtag lines from Bloomington and try your method to get good BRP patterns.

Of course I can recommend these. But if you try the Janelia fly light 5d nc82 protocol it should work. Best,

Greg b