mardtb 248x110
Edited on 19-May-2023

CSC (Cryogenic Sample Changer)

1. Introduction


The "CSC"-page can be accessed by selecting the corresponding tab in the main window or by pressing the "Ctrl+0"-key while the pointer is in the main window. The page is available only if the configuration file carries the line CSC USE (see chapter Configuration File in section Input). Here, you can access all functions of the optional sample changer.

The "CSC"-page features several work areas:

1.1 Principles of Operation

The cryogenic sample changer (CSC) is an extension of the desktop beamline. In total, 7 motors are added to the dtb (see chapter Motors in section Introduction), but they are all driven by the same dtb controller. Changing a sample is a complex sequence of individual motor movements, where one step usually relies on successful completion of a previous step, i.e. it requires exact synchronisation of all participating components. The process of loading a sample, for instance, is a sequence of approx. 30 individual steps. Fortunately, there are only 2 variable parameters for that entire process:

The carousel in its current implementation holds 19 samples. It is possible to replace the entire carousel or to replace only single vials in the carousel by new ones. This is described further down in the chapter CSC Operations.

2. CSC Menu

The "CSC"-menu pops up if the "CSC"-button in the menu bar is pressed or if "Alt+c" is pressed while the pointer is in the main window. This menu allows for accessing different options that have to do with the sample changer. The choices are:

Table 1: The "CSC"-menu

Menu Menu Choice Description
CSC Menu Load carousel data Loads a sample status file. For details, refer to chapter Sample Status File in section Input).
Save carousel data Saves current sample status in an ASCII-file (see above).
Clear carousel data Clears all entries of sample status.
Release magnet The magnet holding the loop on the goniometer head is turned off.
Energize magnet The magnet holding the loop on the goniometer head is turned on.
Transfer xyz from mounted sample to Crystal page This copies the stored xyz-coordinates of a previously mounted sample into the fields for X,Y,Z-translations on the Crystal page. Saves some typing...
Move sample to stored position A sample is moved to the previously determined and stored xyz-coordinates. Useful after remounting a sample.
Unload sample at end of data collection When checked, the crystal is put back into the carousel after finishing data collection. When unchecked, it stays on the goniometer head.

3. CSC Operartions

CSC: Operations

3.1 Change Sample

This procedure implies that a sample is currently mounted. This sample is then going to be stored in the carousel and a new sample is mounted from the given carousel position.

Besides providing the desired carousel position, the pin length has to be provided. The pin length plays a critical role at the time when the pin containing the sample is transferred from the SERVER motor onto the goniometer head, since it involves a motion of the z-translation of the goniometer head. from the barcode. The pin length can be obtained from the barcode in those cases where the structure of the barcode really does contain that information. Otherwise, it has to be provided. It should be noted that if the barcode is unreadable the choice for automatically obtaining the pin length from the barcode is an error condition. The consequence is that the samplee in that case will NOT be mounted but stored back in the carousel. It is therefore safer to provide the pin length explicely provided it is known!

3.2 Load Sample

This procedure implies that no sample is currently mounted. A new sample is mounted from the given carousel position. The pin length will be considered as described in chapter Change Sample.

3.3 Unload Sample

The currently mounted sample will be stored in the carousel position that is currently indicated in the status area. The value provided in the text field on the right hand side of the button is meaningless.

3.4 Give Vial

The purpose of this operation is to remove a sample from the carousel. It may serve as a component of carousel refill. Please note, that this operation may be carried out while a sample is mounted and even while a data collection is running, i.e. it does not interfere.
The vial from the give carousel position will be taken out of the carousel and presented to the user. The user may grab the vial and transfer it into a transport container or elsewhere.

3.5 Take Vial

The purpose of this operation is to insert a new sample into an empty position of the carousel. It is the reverse action of the previous operation. A user inserts a vial (enclosed in a transfer container) in the holding brackets of the SERVER. The vial is then transferred to the given position of the carousel.
Both operations (Give and Take) can also be handled by the remote control unit.

3.6 Move sample to stored xyz during LOAD

When remounting a sample that has already been centered on the goniometer head it is useful to use the already known xyz-coordinates that have automatically been stored in the previous centering operation. This will leave the sample at or at least very near its center. Please take care, though, that you turn off this option if you mount a new sample that happens to be in the same carousel position as another sample. The xyz-coordinates of the previous sample will not be valid for the new sample. But the sample changer has no intrinsic knowledge of the fact that the samples have been changed. As by version 5.2, the mar345dtb program does not compare the barcode of the current sample with the one of the previously mounted sample!

3.7 Shift Corrections

With the second generation of sample changers, the carousel has been redesigned and makes use of little magnets to keep the vials in place. While this construction is more forgiving to small variations of vial shapes, it allows for more freedom of rotation. The net effect is that it is not longer guaranteed that sample xyz-coordinates that have been determined once, are still valid when the sample is stored back into the carousel and taken out again by the sample changer. Small shifts and rotations may occur that will leave the sample eventually slightly out of the beam after mounting it on the goniometer head.

A special procedure has been implemented to compensate for this mechanical problem. The way it works is the following:

All this is being done automatically without user intervention, but only if the box "Use shift corrections" is checked. This checkbox is available only if the configuration file carries a line "CSC   SHIFT" (see chapter Configuration File in section Input).

Usage of this procedure implies that images of the crystal are taken in certain intervals in order to be able to do a comparison later on. Also this is done automatically without necessity of manual intervention.

4. Initialize

CSC: Initialize

The sample changer heavily relies on the error-free sequence of a large number of individual tasks. In real life, errors do occur due to various reasons. In most cases it will be necessary to reinitialize the sample changer to recover from a hardware error. The initialization will bring all CSC components back into a known state. The initialization routines work without variable parameters which make them straightforward to use. The initialization is divided into groups of motors which have to be initialized together, since motions or positions of some motors may depend on the ones from other motors:

Usually, an initialization of all CSC-components is the simplest thing to do but there is a choice of only initializing one particular group.

5. CSC Options

CSC: Options

In the options area you can

The barcode reader is an important component of the sample changer. It allows for safe identification of the samples, but it also adds security to the instrument and potentially avoids crashes. Let us assume, that a sample is mounted on the goniometer head. You then tell the sample changer to unload the sample and store in the vial in carousel position 5. The sample changer now takes the vial out of the carousel and moves it to the barcode reader. The barcode reader now finds one out of 3 different scenarios: In this particular situation, if the barcode reader identifies a cap (either with or without barcode), the sample changer would produce a crash and lose the currently mounted sample if it would procede with the UNLOAD procedure. The only safe operation in this situation is to put the vial back into the carousel and wait for user action.

To prevent possible crashes, it is therefore generally advisable to choose the option "Stop on CRITICAL barcode errors". The alternative would be to ignore all or to stop also on non-critical errors. A non-critical errors would be the inability to identify the barcode itself. This is something that might happen due to a bad barcode on the cap or due to too much liquid nitrogen floating on the cap. This kind of error should not be regarded as a problem, and therefore it is not recommended to let the sample changer also stop on this error. On the other hand, ignoring all errors is a security risk and has the potential to crash crystals and even to produce hardware crashes.

The second option is to teach the dtb that a certain sample is loaded or that no sample is loaded. When manually removing a sample from the goniometer head or mounting a sample onto the head, there will be no electronical feedback. The controller has to be told explicitely what has been done.

6. Carousel Status

CSC: Carousel Status

The status area shows and stores information about available vials in the carousel. The contents of this window are regularly updated as soon as a bit of information changes, e.g. if a barcode is read or if a new crystal center is found. The window keeps track of the following elements for all 19 samples of the carousel:

Element Description
Status One of: "mounted", "carousel" or "empty"
Barcode Barcode of sample (optional)
Identifier Optional identification string for the sample
Pin length Either 14, 16,18,21,24 or 0 mm (with 0=automatic)
Crystal center x,y,z Positions of xyz-translations of goniometer head


The sample status will automatically be saved to an ASCII-file called $MARLOGDIR/csc/CSC.csv. It is an Excel-type .csv formatted file. Please see chapter Carousel File in section Output for details.