Decoding the functional connectivity of the nervous system is facilitated by transgenic methods that express a genetically encoded reporter or effector in specific neurons; however, most transgenic lines show broad spatiotemporal and cell-type expression. Increased specificity can be achieved using intersectional genetic methods which restrict reporter expression to cells that co-express multiple drivers, such as Gal4 and Cre. To facilitate intersectional targeting in zebrafish, we have generated more than 50 new Cre lines, and co-registered brain expression images with the Zebrafish Brain Browser, a cellular resolution atlas of 264 transgenic lines. Lines labeling neurons of interest can be identified using a web-browser to perform a 3D spatial search (zbbrowser.com). This resource facilitates the design of intersectional genetic experiments and will advance a wide range of precision circuit-mapping studies.

#### rhombomere

This archive contains:
y454-eltC (Tg(eltC-REx2-SCP1:BGi-Cre-2a-Cer)y454), N = 3 larval zebrafish;
y455-dr16 (Tg(hoxb3a-dr16-SCP1:BGi-Cre-2a-Cer)y455), N = 3;
y461-hoxb1a (Tg(hoxb1a-SCP1:BGi-Cre-2a-Cer)y461), N = 5;
y466-hoxa2 (Tg(hoxa2CNE-SCP1:BGi-Cre-2a-Cer)y466), N = 4.
Image stacks are compressed nifti files (16 bit), labeled as: "line identifier" - "fish #" - "color channel #".
Color channel 01 is Tg(elavl3:mCar.zf1)y583 (huC:mCar), and color channel 02 is the Cre expression pattern.

#### y371-y385

This archive contains:
y371-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y371, N = 4 larval zebrafish;
y378-Cre, N = 3;
y379-Cre, N = 3;
y380-Cre, N = 3;
y381-Cre, N = 2;
y382-Cre, N = 3;
y383-Cre, N = 3;
y384-Cre, N = 4;
y385-Cre, N = 3.
Image stacks are compressed nifti files (16 bit), labeled as: "line identifier" - "fish #" - "color channel #".
For most brain images, color channel 01 is the merged RFP and GFP signals of βactin:Switch (Tg(actb2:loxP-eGFP-loxP-ly-TagRFPT)y272) and channel 02 is the Cre expression pattern (RFP signal).
For y378-f2, y378-f3, y381-f1 and y381-f2 color channel 01 is Tg(elavl3:mCar.zf1)y583 (huC:mCar) and channel 02 is the Cre expression pattern.

#### y445-y459

This archive contains:
y445-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y445, N = 3 larval zebrafish;
y456-Cre, N = 3;
y457-Cre, N = 3;
y458-Cre, N = 4;
y459-Cre, N = 3.
Image stacks are compressed nifti files (16 bit), labeled as: "line identifier" - "fish #" - "color channel #".
Color channel 01 is Tg(elavl3:mCar.zf1)y583 (huC:mCar) and channel 02 is the Cre expression pattern.

#### y465-y481

This archive contains:
y465-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y465, N = 5 larval zebrafish;
y478-Cre, N = 3;
y479-Cre, N = 3;
y480-Cre, N = 3;
y481-Cre, N = 4.
Image stacks are compressed nifti files (16 bit), labeled as: "line identifier" - "fish #" - "color channel #".
For most brain images, color channel 01 is the merged RFP and GFP signals of βactin:Switch (Tg(actb2:loxP-eGFP-loxP-ly-TagRFPT)y272) and channel 02 is the Cre expression pattern (RFP signal).
For y465-f5, color channel 01 is Tg(elavl3:mCar.zf1)y583 (huC:mCar) and channel 02 is the Cre expression pattern.

#### y483-y487

This archive contains:
y483-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y483, N = 3 larval zebrafish;
y484-Cre, N = 4;
y485-Cre, N = 3;
y486-Cre, N = 4;
y487-Cre, N = 3.
Image stacks are compressed nifti files (16 bit), labeled as: "line identifier" - "fish #" - "color channel #".
Color channel 01 is the merged RFP and GFP signals of βactin:Switch (Tg(actb2:loxP-eGFP-loxP-ly-TagRFPT)y272) and channel 02 is the Cre expression pattern (RFP signal).

#### y488-y493

This archive contains:
y488-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y488, N = 3 larval zebrafish;
y489-Cre, N = 4;
y490-Cre, N = 3;
y492-Cre, N = 3;
y493-Cre, N = 3.
Image stacks are compressed nifti files (16 bit), labeled as: "line identifier" - "fish #" - "color channel #".
Color channel 01 is the merged RFP and GFP signals of βactin:Switch (Tg(actb2:loxP-eGFP-loxP-ly-TagRFPT)y272) and channel 02 is the Cre expression pattern (RFP signal).

#### y494-y521

This archive contains:
y494-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y494, N = 3 larval zebrafish;
y495-Cre, N = 3;
y519-Cre, N = 4;
y520-Cre, N = 3;
y521-Cre, N = 3.
Image stacks are compressed nifti files (16 bit), labeled as: "line identifier" - "fish #" - "color channel #".
Color channel 01 is the merged RFP and GFP signals of βactin:Switch (Tg(actb2:loxP-eGFP-loxP-ly-TagRFPT)y272) and channel 02 is the Cre expression pattern (RFP signal).

#### y523-y541

This archive contains:
y523-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y523, N = 5 larval zebrafish;
y524-Cre, N = 3;
y526-Cre, N = 3;
y528-Cre, N = 3;
y541-Cre, N = 4.
Image stacks are compressed nifti files (16 bit), labeled as: "line identifier" - "fish #" - "color channel #".
Color channel 01 is the merged RFP and GFP signals of βactin:Switch (Tg(actb2:loxP-eGFP-loxP-ly-TagRFPT)y272) and channel 02 is the Cre expression pattern (RFP signal).

#### y542-y546

This archive contains:
y542-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y542, N = 4 larval zebrafish;
y543-Cre, N = 4;
y544-Cre, N = 4;
y545-Cre, N = 10;
y546-Cre, N = 5.
Image stacks are compressed nifti files (8 bit), labeled as: "line identifier" - "fish #" - "color channel #".
Color channel 01 is the merged RFP and GFP signals of βactin:Switch (Tg(actb2:loxP-eGFP-loxP-ly-TagRFPT)y272) and channel 02 is the Cre expression pattern (RFP signal).

#### y547-y552

This archive contains:
y547-Cre Et(REx2-SCP1:BGi-Cre)y547, N = 4 larval zebrafish;
y548-Cre Et(REx2-SCP1:BGi-Cre)y548, N = 4;
y549-Cre Et(REx2-SCP1:BGi-Cre)y549, N = 5;
y550-Cre Et(REx2-SCP1:BGi-Cre)y550, N = 4;
y551-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y551, N = 4;
y552-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y552, N = 4.
Image stacks are compressed nifti files (8 bit), labeled as: "line identifier" - "fish #" - "color channel #".
Color channel 01 is the merged RFP and GFP signals of βactin:Switch (Tg(actb2:loxP-eGFP-loxP-ly-TagRFPT)y272) and channel 02 is the Cre expression pattern (RFP signal).

#### y553-y558

This archive contains:
y553-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y553, N = 6 larval zebrafish;
y554-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y554, N = 4;
y555-Cre Et(REx2-SCP1:BGi-Cre)y555, N = 3;
y556-Cre Et(REx2-SCP1:BGi-Cre)y556, N = 4;
y557-Cre Et(REx2-SCP1:BGi-Cre)y557, N = 5,
y558-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y558, N = 4.
Image stacks are compressed nifti files (y557 is 16 bit, others are 8 bit), labeled as: "line identifier" - "fish #" - "color channel #".
Color channel 01 is the merged RFP and GFP signals of βactin:Switch (Tg(actb2:loxP-eGFP-loxP-ly-TagRFPT)y272) and channel 02 is the Cre expression pattern (RFP signal).

#### y559-y574

This archive contains:
y559-Cre Et(REx2-SCP1:BGi-Cre)y559, N = 4 larval zebrafish;
y568-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y568, N = 6;
y569-Cre Et(REx2-SCP1:BGi-Cre)y569, N = 7;
y570-Cre Et(REx2-SCP1:BGi-Cre)y570, N = 5;
y571-Cre Et(REx2-SCP1:BGi-Cre-2a-Cer)y571, N = 8,
y574-Cre Et(REx2-SCP1:BGi-Cre)y574, N = 4.
Image stacks are compressed nifti files (8 bit), labeled as: "line identifier" - "fish #" - "color channel #".
Color channel 01 is the merged RFP and GFP signals of βactin:Switch (Tg(actb2:loxP-eGFP-loxP-ly-TagRFPT)y272) and channel 02 is the Cre expression pattern (RFP signal).