View source for GRIN Lens Information

[[File:GRINProfil.png|thumb|300px|Example index of refraction profile of a 2mm diameter lens.]]
GRadient INdex (GRIN) lenses use a non uniform index of refraction to shape light instead of surface curvature as with standard lenses. Our system uses a cylindrical GRIN lens which is implanted within 200um of the structure of interest. For a given GRIN lens, its focusing property can be adjusted by changing the pitch of the lens which is directly related to the lens length.
*Advantages of GRIN lenses
**Extremely small to zero working distance
**Optical properties tune-able by changing lens length
**Affordable
**Small size (down to 0.5mm in diameter)
**Compatible
*Disadvantages of GRIN lenses
**No optimal index of refraction profile for imaging applications
**The majority of commercially available GRIN lenses are not optimized for imaging applications (discussed below)
**People have experienced supply issues from some suppliers (discussed below)

Our system currently uses a 0.25 pitch GRIN lens along with an achromatic lens to form an imaging on the microscope's imaging sensor. Sliding the imaging sensor up or down will shift the focal plane in the brain. We have successfully imaged hippocampus CA1, visual cortex, and subiculum using 2mm and 1.8mm diameter GRIN lenses. We are now in the process of testing smaller diameter relay lenses which will work in conjunction with the larger 0.25 pitch lens.
== GRIN Lens Optics ==
A nice overview of GRIN optics can be found on [[https://en.wikipedia.org/wiki/Gradient-index_optics|wikipedia]] and [[http://www.grintech.de/gradient-index-optics.html|Grintech.de]]. The most common use for GRIN lenses is for fiber coupling and light collimation and focusing. Aside from Grintech, all other GRIN lens manufacturers appear to produce GRIN lenses mainly for this use and not specifically for imaging. The index of refraction profile for most commercial GRIN lenses follow a second order expansion of a hyperbolic secant curve. The second order expansion (a parabola) is the ideal profile for on axis focusing of collimated light but has focusing issues of off axis light. Grintech uses an additional manufacturing step to add the forth order expansion term of the hyperbolic secant to their index of refraction profile. The forth order term improves off axis focusing which is very important for imaging applications. Theoretically there is not an ideal index of refraction profile for an imaging GRIN lens but the 4th order expansion term does a good enough job for imaging in our system.

Information about GRIN lens optics and manufacturing is a bit hard to find. We have listed a few papers below which provide nice incite on the topic
*Analysis of Refractive Index Distributions in Cylindrical, Graded- Index Glass Rods (GRIN Rods) Used as Image Relays
**E. G. Rawson, D. R. Herriott, and J. McKenna
**March 1970 / Vol. 9, No. 3 / APPLIED OPTICS
*Diffraction-limited gradient-index (GRIN) microlenses with high numerical apertures produced by silver ion exchange in glass: diffusion modeling and process optimization
**Bernhard Messerschmidt, Ulf Possner, Albrecht v. Pfeil, and Torsten Possner
**SPIE Vol. 3424 s 0277-786X/98
*Fabrication of gradient refractive index rod lens using double ion exchange processes
**Hao Lv, Aimei Liu, Jufang Tong, Xunong Yi, Qianguang Li, Xinmin Wang, Yaoming Ding
**Optical Engineering 50(7), 073402 (July 2011)
*

== GRIN Lens Issues ==
As mentioned in the section above, the majority of commercially available GRIN lenses are manufactured with a second order sech profile causing poor off-axis focusing. While these lenses can resolve similar sized objects as forth order sech profile GRIN lenses they have much lower contrast. This is due to some angles of a point source of light not being focused to the same 3-dimensional spot as other angles of light from that same point source. This results in a nicely resolved image generated by some angles of light with a diffuse glow of light generated by other light angles. This proves to be a reasonably big issue when imaging neural activity since the unfocused, diffuse glow produced by most GRIN lenses increases your measured background fluorescence, making it difficult to pull out dF/F activity.

Currently there seems to be only one manufacturer, Grintech, that produces GRIN lenses with a 4th order index of refraction profile. Additionally, Grintech uses an ion exchange process that has been certified to be bio-compatible. That being said, we have heard from many people that it can be difficult to get lenses from Grintech due to production limitations or exclusive sales agreements. For that reason we are actively working with other GRIN lens manufacturers to modify their product lines to produce high quality imaging GRIN lenses. More information on this topic can be found in the section below.

== GRIN Lens Manufacturers/Suppliers==
There are three major manufacturers of GRIN lenses world wide.
;Grintech
:Currently Grintech produces the best lenses for imaging applications but many people have experienced supply issues with them. The work presented on this site has all been done using Grintech lenses.
;Go!Foton (NSG)
:Likely the largest manufacturer of GRIN lenses. Their product lines are mainly aimed at telecommunication applications and fiber coupling. They do sell an 'imaging' version of their lens and we are actively testing out these new lenses. We are also working with them to modify their production lines to produce high quality imaging GRIN lenses.
;Altechna/Chinese manufacturing 
:Altechna is a Lithuanian company with manufacturing in China. We have been in talks with them to improve the imaging properties of their lenses.

== GRIN Lens Specifications for the Miniscope System ==
*Our system currently uses 2mm and 1.8mm diameter GRIN lenses with a pitch of (0.25 + 0.5*N), where N is an integer.
*We have successfully used 1.8mm and 2mm GRIN lenses from Grintech (which are about 4mm to 5mm in length) to image hippocampal CA1. Their respective part numbers are GT-IFRL-180_inf_50-NC and GT-IFRL-200_inf_50-NC. The slightly longer length of the 2mm diameter GRIN lenses make them a bit easier to use.
*GRIN lenses with a 4th order index of refraction profile will image significantly better than 2nd order lenses.
*The overall length of your GRIN lens should stick far enough out of the skull to allow you to hold it during implantation and cement it to the skull.
*The distance between the top of the GRIN lens and other miniscope optics is not too critical. You will want to cement the baseplate so that the top of the GRIN lens is somewhere between the bottom of the scope body and the internal dichroic mirror.
*For GRIN lenses smaller than 1.8mm in diameter, a GRIN relay lens should be used as the implanted lens and then imaged with a  2mm diameter GRIN lens. We are currently working on this.