HiSeq2000 - Next Level Hacking


Hi @kaspar
Yes, this is very scientific :slight_smile: The two cameras are connected to the electronics by only quite fragile flat wires, so best to keep the tape that I put. Once you have the frame grabber card, you need to connect the camera to the card with the cable that @tboysen sent you. Then find a way to power the camera with +/- 15VDC and 5VDC (about 0.5-1 Amper each). With the Hamamatsu HCImage software ( https://dcam-api.com/hamamatsu-software/ ) you should see both cameras and be able to take images from both cameras. If you switch to TDI mode you need to select “internal trigger” (on the HiSeq the FPGA generates the trigger). Remember you will only see some lines as this is a line camera - you should see changes in brightness if you cover the slit :wink: . I tested this and it worked for me. And then you can start playing with drivers.

Have fun.

PS: ChaosLooper is also on it’s way.


Welcome to the forum, @RSpanish ! See post by jmarkham earlier in this thread for a comparison of HiSeq2000 vs HiSeq 2500.


Hi @RSpanish, regarding possible contributions, I can propose some things that I think would be useful, but I will leave it for others to comment. Also I’m not sure if you have students/time available so I’m just making this up as I go…

A diagnostics program would be handy. By that I mean something that can find out what drivers and hardware are installed on an instrument and then talk to all the different components to ask them what their firmware version is and see if they respond appropriately when asked to do some kind of action. The machine I have was retired after it failed and something like this would have been useful for troubleshooting.

I’m keen on controlling the microscope using micro-manager (open-source fully functional microscope control software). That would require device adaptors in C++ to control at least the microscope parts (x,y,z,lasers,cameras). In principle it could control all manner of things if it had the device adaptors. MM can also just be used as an API by other programs.

Regardless of whether MM is ultimately used, both the diagnostics and the program that drives the instrument could call low level functions that talk to the hardware - mostly via RS-232 with vendor-specific command sets.



Hello All! I am a fourth year undergraduate student at a university in the USA. Chiefly, I just wanted to let you guys know that the information that you guys have been posting is SO INCREDIBLY helpful for my Instrumental Analysis course. I am so lucky to have stumble upon the Hacketeria website where I was able to find a block diagram of Illumina’s HiSeq instrument and images if the instrument components itself. This data has been so hard to find. Moreover, I have been having trouble finding information about the fluorescence that is used on the nucleotides. Does anyone know what is used?



The excitation is done at 532 and 660nm, from a discussion about dyes
some months ago i remember these dyes were used in a Illumina 4-channel
SBS kit:

Alexa 647-dATP

The last dye i don’t know, should be found out by seaching in the
patents Illumina is citing. Hope this is correct…



Ok, @kaspar @jmarkham @bengtsjolen . For the HiSeq meeting at GaudiLabs, 8.-10. January 2019 (Tuesday-Wednesday) it is. I am really looking forward to us meeting around this exciting project and making an other step forward. I am happy to host you in the lab (have mattresses and sleeping bags) and in my place (very close to the lab). Plan your travel individually (you find GaudiLabs on Google Maps). We can later decide if we want to put the expenses in the crowdfunding budget.

Program suggestion:

- Make work the hacked machine
- Experiment with fluorescent scanning and other potential applications
- Think about software, interface and implementations
- Design crowdfunding and shoot a video

What else? What do we need to prepare?


I have booked my flights! I will be flying to Basel in the evening on 6th of January I can take the train to Luzern or Zurich from there depending on plans. I’ll be off again on the 13th.