Robotics and process development for MX and Cryo-EM
Central information page for the implementation of the eCryoID tracking system.
The eCryoID consortium have been created by EMBL Grenoble Instrumentation group in order to bring together the manufacturers of eCryoID equipped devices and to centralise the attribution of Manufacturer IDs and Device Type codes.
The consortium is today composed by the following members:
To join the consortium or to request for the attribution of new Manufacturer IDs and Device Type codes please Contact us.
The memory of the eCryoID tag is organized in 52 pages. One page can store 4 bytes (32 bits) and ASCII encoding (4 characters/page) was choosen for the programming of the RFID tags.
The pages are devided in three main domains:
The Device UID has been defined to avoid duplicated IDs between different manufacturers. It is composed of 8 alphanumerical characters. Only six characters are used, the last two being reserved for future extension.
The first letter of the Device UID is the manufacturer ID. It is attributed according to the Manufacturer Ids table here after. It is up to each manufacturer to follow up on the distribution of the remaining 5 characters, to ensure unique IDs in its production.The Device UID is stored in the memory Pages 0 and 1 of the eCryoID tag that contain 8 characters in total. Space characters (ASCII character: 32 decimal base, 20 hexadecimal base) should complete the 6 UID characters to reach a total of 8 characters.
Example for the device UID “AX123A” we have to write “AX123A ” into the chip.
| | Page 0 | Page 1 |
|---|---|---|
| ASCII Character | A X 1 2 | 3 A |
| Hexadecimal Code | 0x41 0x58 0x31 0x32 | 0x33 0x41 0x20 0x20 |
| Manufacturer Name | Manufacturer ID |
|---|---|
| Mitegen | B |
| Molecular Dimensions Ltd | C |
| Hampton Research | H |
| Marresearch GmbH | M |
| Reserved for internal tests | A,Z,E |
The device type allows automated handling systems to recognize a device, e.g. in MX, the different pucks that fit in the same Dewar slot. The device type is stored in the memory page 2 of the RFID chip, which contains 4 characters in total. The currently available device type codes are summerized in the table Device Type Codes.
Example: For an SC3 puck , the code “MX0 “ has to be written to the page 2 of the RFID tag
| | Page 2 |
|---|---|
| ASCII Character | M X 0 |
| Hexadecimal Code | 0x4D 0x58 0x30 0x20 |
| Device Type | Device Type Code |
|---|---|
| SC3 puck | MX0 |
| uni-puck | MX1 |
| SPINEplus puck | MX2 |
| miniSPINE puck | MX3 |
| NewPin36 puck | MX4 |
| NewPin64 puck | MX5 |
| Cryo-EM puck (MiTeGen design) | MP1 |
| Cryo-EM puck (Subangstrom design) | MS1 |
| Cryo-EM box (EMBL EasyGrid design) – 1 | EB1 |
The used field can be used for any purpose. It starts on Page 3 and ends on Page 51.
On the table below we show an encoding example:
To help the wide-spreading of the eCryoID identification technology the EMBL Grenoble Instrumentation Team has created the easy to use, easy to integrate eCryoID reader/writer device. This device permits to read and write the eCryoID tags respecting the above described protocol. There are various accessories to adapt the reader to different device types (a couple of examples on the following pictures). The eCryoID reader runs a web interface accessible from a simple browser (no software installation required). Furthermore it also runs a low level socket server permitting to integrate it into bigger systems using machine to machine communication.
For more information please contact us.
The eCryoID reader/writer can be updated in order to support new manufacturer IDs ans device type IDs. In order to keep a coherence over these different codes and avoid duplicates, the latest configuration files of the devices are availables exclusively on this website.
To proceed to the update of your device please download the latest configuration package from the list below and upload it to your CryoRFID reader device using the web interface.
Please contact us by mail cryorfid@embl.fr
Latest Website Updates:
15 Feb 2021: Migration to WordPress
28 Apr 2020: Page creation
SPINE Contract QLG2-CT-2002-00988
2014 April 15th – SPINE SAMPLE HOLDER & VIAL SPECIFICATIONS-L-R05: In order to extend the handling possibilities of the Spine sample holder the dimensions of the Cap are completed/clarified (in red)
SPINE_SAMPLE_HOLDER_+_VIAL_SPECIFICATIONS-L-R05
SPINESpecs-L-R04_ComplementaryData-R02
DM_16001_A-_Sample_holder_+_vial
DM_16210_A_-_VialDM_16300_-_Goniometer_mount
SPINE_SAMPLE_HOLDER_+_VIAL_SPECIFICATIONS-L-R04
Latest Website Updates:
15 Feb 2021: Migration to WordPress
20 Apr 2020 : Changing css sheet of the webpage
15 Apr 2014 : Adding SPINE SAMPLE HOLDER & VIAL SPECIFICATIONS-L-R05
This page is regularily updated with the latest developments
In 2009 a feasibility study for a new sample holder standard with high sample storage density and precise sample positioning was launched at the EMBL Grenoble. Since 2011 the project has been supported by the European FP7 program BioStruct-X under the name NewPin (http://www.biostruct-x.eu). Led by the EMBL Grenoble outstation the project numbers six synchrotron partners: DLS, ESRF, EMBL@PETRA-III, HZB-BESSY II, the MAX IV Laboratory and SLS. NewPin is also supported by the US synchrotron NSLS-II and by European and American companies active in the field of consumables and robotics (MiTeGen, Molecular Dimensions, Irelec and Arinax).
Two sample holder models named NewPin and miniSPINE were initially proposed. Both allow the storage of 36 samples in pucks with a uni-puck style footprint. A robot gripper that acts as a cold buffer can manipulate both the miniSPINE and NewPin sample holders.
A puck and a robot gripper compatible with the SPINE sample holders (SPINEplus) have also been defined to facilitate the migration from SPINE to miniSPINE and NewPin.
Initial evaluation of miniSPINE and NewPin was made at the EMBL ESRF/GRG beamline BM14 using a robotic setup based on a six 6 axis industrial robot, a compatible robot gripper and a Dewar (FlexED8: the first member of a fast and flexible sample-changer family for macromolecular crystallography, 2017, Acta Cryst. D73, 841-851 ).
The miniSPINE model has been selected for the medium scale evaluation of the new standard as it is easier to integrate into beamlines. miniSPINE Evaluation Kits were proposed to evaluate the manual use of the miniSPINE sample holders.
The NewPin model will offer high precision sample positioning and the possibility to increase storage density to 64 pins per puck (fully robotic handling only). The pins will be optionally identified with RFID transponders (under development). The NewPin model will be further evaluated in a second round.
Details of former developments are available here.
The standard defines the main dimensions of the sample holder base and associated puck and identification schemes.
The miniSPINE Pin base is a 7 mm diameter ferromagnetic support with 1.9 mm diameter gripping area. The basic Pin model is compatible with 0.65 mm diameter cryo-mounts. The dimensions of the Pin base make the miniSPINE Pin compatible with Spine-compatible goniometer setups. See goniometer mounts. The miniSPINE Pin bases can be identified with a Datamatrix ID.
Different versions of the miniSPINE Pin base allow:
Holds up to 36 miniSPINE Pins. uni-puck style footprint for compatibility with sample changers that accept uni-puck pucks (Requires specific Dewar slots). Compatible with CX100 transport Dewars. Preliminary information (pdf).
A puck for Robot direct data collection is under development (DDC puck).
For more information please contact newpin@embl.fr
To facilitate the manual harvesting process and manual puck filling:
To extract/insert miniSPINE Pins from the miniSPINE Pucks.
To manipulate the miniSPINE or NewPin pucks and their covers.
To transfer the miniSPINE and NewPin Pins with a 6 axis industrial robot.
For more information please contact newpin@embl.fr or IRELEC-Alcen
Electromagnet with Pin detection. Compatible with Spine and miniSPINE Pins
For more information please contact newpin@embl.fr or Arinax
Recommended Dewar slot for miniSPINE, NewPin and SPINEplus Pucks. Compatible with uni-pucks: Precise puck mounting with accurate puck detection.
Under development: For more information please contact newpin@embl.fr
Under development: For more information please contact newpin@embl.fr
For more information please contact newpin@embl.fr
To avoid duplicates the first character of the codes identifies the manufacturer. It is up to the manufacturers to ensure unique IDs within their production.
| Manufacturer | Manufacturer ID Letter | Manufacturer ID Number |
|---|---|---|
| EMBL (For development purpose) | A | 0 |
| MiTeGen | B | 1 |
| Molecular Dimensions | C | 2 |
Last website updates:
28 Apr 2020, 11:43:23 CEST: Correcting synthax used for uni-pucks
24 Jan 2018, 14:38:11 CEST: New miniSPINE puck filling assistant
13 Oct 2017, 08:45:00 CEST: Full access no longer requires login; Preliminary information PDFs on miniSPINE pins and pucks updated
20 Oct 2016, 15:03:10 CEST: Full access requires login. For mor information, please contact newpin@embl.fr
22 Aug 2016, 15:18:11 CEST: Minor updates
17 Mar 2016, 11:43:16 CEST: Last News, BioStruct-X Wrap-up meeting
07 Mar 2016, 16:28:32 CEST: New versions of miniSPINE pin and puck; Update of the evaluation feedback log