VirtualBrainLab
np2.0 quad 3d model
Hi Dan, I got ahold of the NP 2.0 Quad models - probe and headstage at these links: probe, hs (though I guess the HS is just for your interest since I'm not sure there is a point of doing anything with it). Hope the ".step" file is a useful format. Could you add this probe as an option for the 'add new probe' menu? Thanks!
While I'm adding this I might as well add the ultra probe -- it's a 2.0 base right, but do you have the channel map configuration info somewhere?
No, Ultra is a 1.0 probe. Here are the x ( https://www.dropbox.com/scl/fi/3828z05b1vg2r9u39zcmw/channels.xcoords.npy?rlkey=b4usowmkulyt2ljnyyugh9c4a&dl=0) and y ( https://www.dropbox.com/scl/fi/vbzx5l7l8k9xujp6v7iaf/channels.ycoords.npy?rlkey=m3ymwlid5t5gjcfm7xttslsh1&dl=0) coordinates of the sites (it's just a 48x8 rectangular grid with 5x5 um sites and 1 um gaps for 6 um center-to-center pitch). Those coordinates relative to the bottom corner of the grid - it would be another ~200 um to the tip as in a normal 1.0 probe.
On Tue, Sep 17, 2024 at 9:14 PM Dan Birman @.***> wrote:
While I'm adding this I might as well add the ultra probe -- it's a 2.0 base right, but do you have the channel map configuration info somewhere?
— Reply to this email directly, view it on GitHub https://github.com/VirtualBrainLab/Pinpoint/issues/738#issuecomment-2357458436, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZ5IPYISPTLNQTE4WN7J7LZXD43TAVCNFSM6AAAAABOMYZABOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNJXGQ2TQNBTGY . You are receiving this because you authored the thread.Message ID: @.***>
Hi @dbirman we need this now - is it something @kjy5 can help with? Thanks!!
I'm guessing when I responded last year I was hoping to sneak this into my new probe library, but I haven't had time to prioritize that.
Just putting this straight into the current system is straightforward, I can help Kenneth with how to set it up. @kjy5 do you know how to convert the STEP file to OBJ by any chance? I vaguely remember doing this in the past but I can't remember if I used blender or had to go through a CAD program to get it done.
@nsteinme I'm going to set up the new pinpoint probe library to pull from the spikeinterface probeinterface_library package. Do you know if the new probe you want is already in this list? https://github.com/SpikeInterface/probeinterface_library/tree/main/imec I'm not sure where these 4-digit numbers come from do you?
I don't think it is - looks like we could ask Jennifer - I also don't know exactly what all the numbers mean. but I don't think those files have the geometry of the probe base right? Shanks of Quad are going to be the same as 4-shank 2.0 as far as I understand (so NP2014 should work) but what we need this for is to make sure we can find geometries where the bases don't collide. The 3d files I added here have this.
On Fri, Aug 22, 2025, 13:10 Dan Birman @.***> wrote:
dbirman left a comment (VirtualBrainLab/Pinpoint#738) https://github.com/VirtualBrainLab/Pinpoint/issues/738#issuecomment-3215494313
@nsteinme https://github.com/nsteinme I'm going to set up the new pinpoint probe library to pull from the spikeinterface probeinterface_library package. Do you know if the new probe you want is already in this list? https://github.com/SpikeInterface/probeinterface_library/tree/main/imec I'm not sure where these 4-digit numbers come from do you?
— Reply to this email directly, view it on GitHub https://github.com/VirtualBrainLab/Pinpoint/issues/738#issuecomment-3215494313, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZ5IP6POOBR4KNNBZN7WT33O52LDAVCNFSM6AAAAACEJT7EJKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTEMJVGQ4TIMZRGM . You are receiving this because you were mentioned.Message ID: @.***>
We have the geometries sorted out through the files you sent! I think the concern was whether this new probe has a new electrode layout or things like that we needed to map. This would be the information that these data files would tell us. If it is the case that they use the same layout as the NP2014 then I guess we can use those files...
Yeah expanding on what Kenneth said, I want to pull the channel/shank geometry from this library if possible, headstage/base geometry will come in separately. So the hope is that all probe channel geometry that we might have to deal with are in there. But yeah sounds like we can just make a PR and add it as another option if it's missing based off of the 2014 layout.
Great thanks for clarifying, I think I get it now. So you want to have your 3D file get a name similar to NP2014 and have that correspond to a geometry that's there, right? In that case I think we should contact Bill/Jennifer and ask whether there's an existing code for this probe, just to get it right. I'll email.
Nick
On Fri, Aug 22, 2025 at 1:51 PM Dan Birman @.***> wrote:
dbirman left a comment (VirtualBrainLab/Pinpoint#738) https://github.com/VirtualBrainLab/Pinpoint/issues/738#issuecomment-3215623739
Yeah expanding on what Kenneth said, I want to pull the channel/shank geometry from this library if possible, headstage/base geometry will come in separately. So the hope is that all probe channel geometry that we might have to deal with are in there. But yeah sounds like we can just make a PR and add it as another option if it's missing based off of the 2014 layout.
— Reply to this email directly, view it on GitHub https://github.com/VirtualBrainLab/Pinpoint/issues/738#issuecomment-3215623739, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZ5IP4YAHO56RWVBLRFJHD3O57DRAVCNFSM6AAAAACEJT7EJKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTEMJVGYZDGNZTHE . You are receiving this because you were mentioned.Message ID: @.***>
Dan was on the email but just to record it here: Quad is NP2020.
On Fri, Aug 22, 2025 at 5:17 PM Nick Steinmetz @.***> wrote:
Great thanks for clarifying, I think I get it now. So you want to have your 3D file get a name similar to NP2014 and have that correspond to a geometry that's there, right? In that case I think we should contact Bill/Jennifer and ask whether there's an existing code for this probe, just to get it right. I'll email.
Nick
On Fri, Aug 22, 2025 at 1:51 PM Dan Birman @.***> wrote:
dbirman left a comment (VirtualBrainLab/Pinpoint#738) https://github.com/VirtualBrainLab/Pinpoint/issues/738#issuecomment-3215623739
Yeah expanding on what Kenneth said, I want to pull the channel/shank geometry from this library if possible, headstage/base geometry will come in separately. So the hope is that all probe channel geometry that we might have to deal with are in there. But yeah sounds like we can just make a PR and add it as another option if it's missing based off of the 2014 layout.
— Reply to this email directly, view it on GitHub https://github.com/VirtualBrainLab/Pinpoint/issues/738#issuecomment-3215623739, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZ5IP4YAHO56RWVBLRFJHD3O57DRAVCNFSM6AAAAACEJT7EJKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTEMJVGYZDGNZTHE . You are receiving this because you were mentioned.Message ID: @.***>
Thanks -- I'm going to work on this over the next week, should be straightforward with all the files available.