# HiSeq2000 - Next Level Hacking **URL:** \ **Category:** ReSeq\ **Created:** [February 2, 2018, 11:34am UTC](https://forum.hackteria.org/t/hiseq2000-next-level-hacking/325 "2018-02-02T11:34:05Z")\ **Posts on this page:** 16\ **Page:** 11
**Author:** ![mamaya](https://yyz2.discourse-cdn.com/flex030/user_avatar/forum.hackteria.org/mamaya/32/1025_2.png) [@mamaya](https://forum.hackteria.org/u/mamaya)\ **Post date:** [September 10, 2019, 10:26am UTC](https://forum.hackteria.org/t/hiseq2000-next-level-hacking/325/202 "2019-09-10T10:26:23Z")
Dear Participants in the Science Photo-Marathon, Many thanks for your interest. We are looking forward to welcome you soon! Four cash awards (CHF 500.- each), and four annual passes (to Zoo Zurich) are waiting for you. You will be also granted some free entries to watch the screened films at the Global Science Film Festival ([www.sciencefilm.ch](http://www.sciencefilm.ch)). The registration is still open, so you can bring your relatives and friends (registration is required [https://www.sciencefilm.ch/photo-marathon](https://www.sciencefilm.ch/photo-marathon)). All the very best, Science Photo-Marathon Team – Dr. Samer Angelone University of Zurich [https://www.ieu.uzh.ch/en/staff/member/angelone\_samer.html](https://www.ieu.uzh.ch/en/staff/member/angelone_samer.html) Festival Director Global Science Film Festival [www.sciencefilm.ch](http://www.sciencefilm.ch) Imfeldstrasse 25, 8037 Zurich Telephone: +41 79 232 60 68; Mail: [samer.angelone@gmail.com](mailto:samer.angelone@gmail.com) Ph.D. sc. nat. Biology (Publications: [Google Scholar](https://scholar.google.ch/citations?hl=de&user=D_cThrwAAAAJ) and [ResearchGate](http://www.researchgate.net/profile/Samer_Angelone)) M.A. Film Directing (Films: [www.vimeo.com/samerangelone](http://www.vimeo.com/samerangelone)) M.A. Film Studies ---
**Author:** ![kunal](https://avatars.discourse-cdn.com/v4/letter/k/dec6dc/32.png) [@kunal](https://forum.hackteria.org/u/kunal)\ **Post date:** [September 20, 2019, 3:25pm UTC](https://forum.hackteria.org/t/hiseq2000-next-level-hacking/325/203 "2019-09-20T15:25:11Z")
Hi All, I’ve been working on controlling a HiSeq2500 and this forum has been an immensely helpful resource. I mainly want control of the instrument to do some spatial transcriptomics or proteomic imaging. I successfully got images from the camera using TDIscan and the FPGA/Y-STAGE commands. However I’d like to use the DCAM API instead of TDIscan. I can talk to and configure the cameras with the DCAM API, but the cameras don’t seem to get triggered after using the FPGA/Y-STAGE. The cameras report taking 0 frames after arming the TDI and moving the Y-STAGE. Has anyone been successful in getting scans with the DCAM API instead of TDIscan? ---
**Author:** ![jmarkham](https://yyz2.discourse-cdn.com/flex030/user_avatar/forum.hackteria.org/jmarkham/32/508_2.png) [@jmarkham](https://forum.hackteria.org/u/jmarkham)\ **Post date:** [September 21, 2019, 9:02am UTC](https://forum.hackteria.org/t/hiseq2000-next-level-hacking/325/204 "2019-09-21T09:02:06Z")
You need to set it up to use hardware trigger. I’m away from a computer but can dig up some code on Monday. @kaspar may be able to help as he is working on this at the moment. Regards, John ---
**Author:** ![gaudi](https://yyz2.discourse-cdn.com/flex030/user_avatar/forum.hackteria.org/gaudi/32/21_2.png) [@gaudi](https://forum.hackteria.org/u/gaudi)\ **Post date:** [September 22, 2019, 9:47pm UTC](https://forum.hackteria.org/t/hiseq2000-next-level-hacking/325/205 "2019-09-22T21:47:37Z")
Hi, Gilad E. contacted me with the following request: I’m interested in using different kinds of polymerases during clustering to cluster more complex kinds of DNA with secondary structures that do not cluster on standard Illumina clustering. Do you have any information on: 1) the basic materials (syringes, ports) needed for flowing reagents in and out of the flowcell? 2) How to purchase stand-alone Illumina flow cells? 3) Info on swapping different reagents instead of Illumina reagents in the cBot instrument during clustering? Anyone has an idea? Urs ---
**Author:** ![kunal](https://avatars.discourse-cdn.com/v4/letter/k/dec6dc/32.png) [@kunal](https://forum.hackteria.org/u/kunal)\ **Post date:** [September 23, 2019, 1:55pm UTC](https://forum.hackteria.org/t/hiseq2000-next-level-hacking/325/206 "2019-09-23T13:55:09Z")
Right, so as far I can tell I can set the trigger 2 ways. 1. I can use dcam\_settriggermode with the mode = 1 for internal or the mode = 128 for TDI. 2. I can use dcam\_setgetpropertyvalue with the property id for trigger mode and the property value of either 1 (normal), 3 (PIV/ fast repeat mode), 7 (multigate), or 8 (multiframe). I think I’ve tried all the different combinations. Logically, I thought it would have just been dcam\_settriggermode = TDI, but I haven’t been successful. ---
**Author:** ![jmarkham](https://yyz2.discourse-cdn.com/flex030/user_avatar/forum.hackteria.org/jmarkham/32/508_2.png) [@jmarkham](https://forum.hackteria.org/u/jmarkham)\ **Post date:** [September 24, 2019, 1:52pm UTC](https://forum.hackteria.org/t/hiseq2000-next-level-hacking/325/207 "2019-09-24T13:52:50Z")
[Here](https://github.com/jefferis/micromanager12extras/blob/master/DeviceAdapters/Hamamatsu/Hamamatsu.cpp) is a source file circa 2008 (around the time the camera was released) where you can see how MM did it. Does that help? I’m not sure if this is DCAM-API v4 or not. From memory there may be differences between v4 and what MM used back then. I’m on holiday but can dig harder when I get back next week. Possibly @kaspar can say something more sensible since (hopefully) he is currently working on this. Regards, John ---
**Author:** ![jmarkham](https://yyz2.discourse-cdn.com/flex030/user_avatar/forum.hackteria.org/jmarkham/32/508_2.png) [@jmarkham](https://forum.hackteria.org/u/jmarkham)\ **Post date:** [September 24, 2019, 1:56pm UTC](https://forum.hackteria.org/t/hiseq2000-next-level-hacking/325/208 "2019-09-24T13:56:31Z")
Regarding 2), I think you can buy flow cells from Illumina still. Is that what he meant? Can’t comment on the others. ---
**Author:** ![jmarkham](https://yyz2.discourse-cdn.com/flex030/user_avatar/forum.hackteria.org/jmarkham/32/508_2.png) [@jmarkham](https://forum.hackteria.org/u/jmarkham)\ **Post date:** [September 24, 2019, 2:21pm UTC](https://forum.hackteria.org/t/hiseq2000-next-level-hacking/325/209 "2019-09-24T14:21:28Z")
Looking [here](https://github.com/soleil-ica/Lima-camera-hamamatsu/tree/master/sdk/msvc/include) I’m guessing you’re using v3? I think think this is the version being used in the 2008 code that I linked to. ---
**Author:** ![kunal](https://avatars.discourse-cdn.com/v4/letter/k/dec6dc/32.png) [@kunal](https://forum.hackteria.org/u/kunal)\ **Post date:** [September 24, 2019, 2:50pm UTC](https://forum.hackteria.org/t/hiseq2000-next-level-hacking/325/210 "2019-09-24T14:50:46Z")
If he doesn’t want to use Illumina stage for the flow cell to world interface, I’ve plasma bonded PDMS donuts to glass flow cells to stick tubing into. ---
**Author:** ![Christine](https://avatars.discourse-cdn.com/v4/letter/c/8491ac/32.png) [@Christine](https://forum.hackteria.org/u/Christine)\ **Post date:** [September 28, 2019, 8:19am UTC](https://forum.hackteria.org/t/hiseq2000-next-level-hacking/325/211 "2019-09-28T08:19:28Z")
Hi, It sounds to be a good idea to try to sequence DNA that cannot be sequenced properly with the standard Illumina technology. Sometimes it is difficult to know if the problem comes from the library preparation step, the clustering step, the sequencing step or if it is a mixture of all that… In case it may help to start with, we have here in Paris some old Illumina consumable & reagents for HiSeq2500 mainly and also MiSeq (list below) 1. the basic materials (syringes, ports) needed for flowing reagents in and out of the flowcell? In the rehyb kits (TruSeq Rapid Rehybridization kit) there are seringes and capillaries to fill th flowcells 1. How to purchase stand-alone Illumina flow cells? Usually not possible to buy without the reagents to do the clonal amplification We have some old not used FlowCell (8 lanes for HiSeq2500) 1. Info on swapping different reagents instead of Illumina reagents in the cBot instrument during clustering? Never try to do that… Let me know if some of these reagents may be usefull, because it takes space in our freezers. Best, Christine ![image](https://canada1.discourse-cdn.com/flex030/uploads/hackteria/original/1X/0ee6dd0b3a0a04d15a92300ba9b33d1dc4d6f526.png) Reagents Illumina Reference Expiration date Quantity TruSeq Rapid Rehybridization kit 15038899 03/04/2015 2 HiSeq PE Cluster Kit V4 cBot Box2 of2 15049947 2019/06/21; 2019/06/25; 2019/06/07 3 TruSeq Rapid Duo cBot sample Plate Box 15037579 18/12/2014 4 TruSeq Rapid PE Cluster Kit HS 15033394 03/07/2015 2 HiSeq Rehybridization V4 15049948 13/10/2015 2 TruSeq rapid SBS Kit HS (200Cycls) 15033386 26/05/2015 2 TruSeq Multiplex Sequencing Primer 15017557 18/06/2015 4 MiSeq Reagent kit V3 (150 Cycles) Box 1 of 2 15043893 01/09/2019 1 ---
**Author:** ![mamaya](https://yyz2.discourse-cdn.com/flex030/user_avatar/forum.hackteria.org/mamaya/32/1025_2.png) [@mamaya](https://forum.hackteria.org/u/mamaya)\ **Post date:** [October 25, 2019, 1:28pm UTC](https://forum.hackteria.org/t/hiseq2000-next-level-hacking/325/212 "2019-10-25T13:28:09Z")
Dear All Finally I found out who this ominiouse Christine is. A Meeting in Paris at La Generale with Emanuel Rebus and an enlighting insight in her practice. Hope to see you again. Best to keept good contact with the people in resource. Christine is working for the Institute for rare genetic illnesses, so her offer of all the equipment leftovers is not a scam, she has great experiences. Would be great to somehow involve here in further processes. And, Paris, Lausanne is very close. Nice things to come. all best Maya ---
**Author:** ![mamaya](https://yyz2.discourse-cdn.com/flex030/user_avatar/forum.hackteria.org/mamaya/32/1025_2.png) [@mamaya](https://forum.hackteria.org/u/mamaya)\ **Post date:** [October 28, 2019, 1:22am UTC](https://forum.hackteria.org/t/hiseq2000-next-level-hacking/325/213 "2019-10-28T01:22:03Z")
Hei Christine Have you ever heard about the geneediting comission? [http://nationalacademies.org/gene-editing/international-commission/index.htm](http://nationalacademies.org/gene-editing/international-commission/index.htm) would be interested about your opinion on this. all best ---
**Author:** ![dusjagr](https://yyz2.discourse-cdn.com/flex030/user_avatar/forum.hackteria.org/dusjagr/32/24_2.png) [@dusjagr](https://forum.hackteria.org/u/dusjagr)\ **Post date:** [October 29, 2019, 11:44pm UTC](https://forum.hackteria.org/t/hiseq2000-next-level-hacking/325/214 "2019-10-29T23:44:49Z")
let’s start to seperate this stream into new topics… > **[Crispr-Babys in China - «Diese Art von Experiment darf nicht akzeptabel werden»](https://www.srf.ch/kultur/wissen/crispr-babys-in-china-diese-art-von-experiment-darf-nicht-akzeptabel-werden)** > > Wie kommen Regeln zur Genmanipulation zustande? Und welche Regeln gibt es überhaupt? Fragen an eine Bioethikerin. ---
**Author:** ![mamaya](https://yyz2.discourse-cdn.com/flex030/user_avatar/forum.hackteria.org/mamaya/32/1025_2.png) [@mamaya](https://forum.hackteria.org/u/mamaya)\ **Post date:** [December 21, 2019, 11:56am UTC](https://forum.hackteria.org/t/hiseq2000-next-level-hacking/325/215 "2019-12-21T11:56:23Z")
hei hei, By the end of the year I am updating my last projects and I made some nice documentation on how to hack a science photo marathon. YES WE WON A PRICE! check out the pics here: [https://www.hackteria.org/wiki/ReSeq2000:\_Science\_Photo\_Marathon\_2019#How\_we\_got\_noticed\_and\_came\_up\_with\_the\_idea:](https://www.hackteria.org/wiki/ReSeq2000:_Science_Photo_Marathon_2019#How_we_got_noticed_and_came_up_with_the_idea:) See you all in Leipzig, motherfuckers! ---
**Author:** ![kaspar](https://avatars.discourse-cdn.com/v4/letter/k/5f8ce5/32.png) [@kaspar](https://forum.hackteria.org/u/kaspar)\ **Post date:** [March 10, 2022, 2:59pm UTC](https://forum.hackteria.org/t/hiseq2000-next-level-hacking/325/216 "2022-03-10T14:59:12Z")
Split this topic on March 10, 2022, 2:59pm UTC A post was split to a new topic: [Editing Illumina recipes/run files](https://forum.hackteria.org/t/editing-illumina-recipes-run-files/1565) ---
**Author:** ![kaspar](https://avatars.discourse-cdn.com/v4/letter/k/5f8ce5/32.png) [@kaspar](https://forum.hackteria.org/u/kaspar)\ **Post date:** [March 10, 2022, 3:00pm UTC](https://forum.hackteria.org/t/hiseq2000-next-level-hacking/325/217 "2022-03-10T15:00:39Z")
Closed on March 10, 2022, 3:00pm UTC [Previous page](https://forum.hackteria.org/t/hiseq2000-next-level-hacking/325.md?page=10)