Collect Tab
The Collect Tab is used for collecting test images and complete monochromatic,
SAD and MAD data sets. Multiple run windows can be set up by creating
additional Run Tabs.

Data collection runs
- The Run tab 0 is the only run displayed when the collect
tab is first opened. It is a special run, dedicated for taking single test images in order to test
crystals and plan strategies for data collection. Only one image at
one time can be collected from this run, so it is not possible to
enter an end frame, although the drop down menu arrow next to the
phi value can be used to quickly set up image collection at 90
degrees away from the first image. A resolution
predictor widget displaying the resolution limits for the selected values of the detector, beamstop distance, and wavelength is available for this tab.
- To create additional data collection run, click on the
'*' tab below the '0' tab. Runs numbered 1
and above can be used to collect complete data sets at multiple energies.
Note: When you create a new "run", the contents
of the old run are automatically copied to the new run.
- An alternative way to collect test shots and generate data collection runs is by using
the Web-Ice strategy calculation. To access this tool, click the
Web-Ice Strategy button. This will open a browser and start
Web-Ice. See the Web-Ice documentation.
Note: Data collection runs exported from Web-Ice can be paused, reset,
modified or aborted from Blu-Ice.
- There is a limit of 17 runs that can be defined, independently
of whether they are generated in Blu-Ice or via Web-Ice. Once this
limit is reached, you must delete old runs in order to define new
ones. Data already collected in not affected by erasing the run.
Data collection parameters and commands
Click on the links above for information on each parameter or input window.
- If you input data collection parameters by hand
(instead of importing them from Web-Ice) make sure that you do
not exceed the particular motor range. You can avoid this by
selecting values within the range defined by the drop-down
menu next to the input box. If you select a value outside this
range, the name of the parameter will be highlighted in
red. You will not be able to initiate the data collection.
- A motor or parameter value displayed in red indicates
that the motor is in a different position. The motor will move to
the position in red upon starting data collection.
- If you click on Default, the current values of distance, axis and energy will be selected
and displayed. In addition, prefix will be set to 'xtal',
directory to '/data/username'. The default detector mode, delta phi and
exposure time are different for each beamline.
- Click on Update if you wish to use the
current motor positions for the data collection. This is
useful if you have already set up the correct detector or
beamstop distance from the Hutch Tab. If you have mounted a
sample using the screening tab, update will also change the directory and image
prefix names to the ones defined in the screening tab. Similarly, if you have
done a MAD scan in the Scan Tab,
the optimal energies for a MAD experiment will be copied to
the run.
Important: Do NOT click on the Update button once
you have finished editing the collection run. This will
cancel all your edits.
- Use the Delete button to delete the run that you
are in. You cannot delete Run 0. Be careful when using this
command. Once a run is deleted, you cannot return to it.
- Use the Reset button to re-use a run. If you do
this you should change the image name or the destination
directory. If you do not change the names, Blu-Ice will create
a subdirectory called OVERWRITTEN_FILES where the old files
will be stored. This will protect the images from one
accidental overwrite.
- Another use of the Reset button is to edit data
collection parameters after stopping a started run (for
instance, to change the detector position). Note: if you
click "Collect" immediately after editing the run, data
collection will restart on the first image again. In order to
continue collection at the current frame, double-click on the
image name as explained in the Tips.
prefix
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- Filename root or file prefix
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directory
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- Shows the directory in which the image will be
saved. Only directory paths starting with "/data" are allowed. When
you select this input box, a list of all the subdirectories in the
current directory will be displayed as a drop-down menu. You can
either select one of the existing directories, or type in a brand new
one.
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beam size
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- Beam size enables inputting various beam sizes for the
data collection. Please see the Adjusting Beam Size section
in the Sample_tab for more information.
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detector
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- Specific values for the detector depends
on the type of detectors. SSRL beamlines use Q315 and MAR325
CCD detectors and Dectris Pilatus 6M and Eiger 16M detectors.
- The ADSC Q315 detector can be used in
"binned" and "binned dezing" modes. Unbinned
images are not supported (they are 4 times the size at no
significant gain in spatial resolution on a typical SSRL beamline)
- In "dezinger" mode two images are collected with half the entered exposure time and the pixel values for each image are compared. If one pixel is a zinger, instead of using this pixel from this image, the software doubles the corresponding pixel value for the other image. Otherwise, the pixel values for both images are added to produce a final image.
- Use dezinger mode if your exposure time is greater than 20-30 seconds.
- The MAR325 detector can be used in "normal" and "dezingered" modes.
- The Pixel Array Detectors (Pilatus and Eiger)
support shutterless data collection in which the shutter does not
close for image readout except for the last image in a run or a
wedge (if the run is being divided in multiple wedges) or before
collecting inverse beam images. This works because the readout time is
mcuh shorter than the time taken to expose each frame. See
information below about pausing the run in shutterless collection mode.
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distance
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- Distance between detector and sample in millimeters; the
minimum distance is usually between 90 and 110 mm, depending
on the beamline.
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beamstop
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- Beamstop distance in millimeters. The optimal beamstop to
sample distance can be determined with Web-Ice
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attenuation/transmission
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- Beam attenuation or transmission. Use to avoid overloaded spots when
collecting low or medium resolution data from strongly
diffracting crystals.
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axis
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- Phi is the only choice unless the beamline is
equipped with a Kappa diffractometer.
- When Kappa is not set to zero, you must collect using Omega.
- The rotation range of Omega is limited.
- On beamlines with a Kappa diffractometer Omega and Kappa are usually locked to prevent hardware
collisions, but can be unlocked if the experiment requires it: contact your support staff.
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delta
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- Oscillation length per image. For the Pilatus
and Eiger detectors a small delta (0.1 or 0.2 degrees) is
recommended because it improves the data statistics and the
detector readout time does not add up anything to the total collection time.
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time
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- Length of exposure time in seconds. It is
strongly recommended to use Web-Ice to estimate
the optimal value. Note that if you change the oscillation angle per
image, the exposure time should be changed by the same factor
to obtain an equivalent exposure per image.
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start
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- The number and phi value assigned to the first image.
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end
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- The number and phi value assigned to the final image.
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inverse beam
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- Rotates the crystal by 180 deg to collect the Friedel pairs for the input phi range.
- When inverse beam is used for a MAD experiment, the inverse beam
pass is collected before changing the energy.
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wedge
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- The phi rotation range that is collected
consecutively before rotating the crystal by 180 degrees (with inverse
beam) or changing energy (during Multi-wavelength experiments).
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energy
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- Energy or energies used for the experiment. As
you enter an energy value, an empty box appears for further energy
entries. The energy boxes can be auto-filled by clicking on the
Update button after doing a MAD scan. If you wish to skip one
or two of the selected energies, simple delete the value.
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take microspec snapshot during run
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- This option is available when enabled from the
Microspec Tab on beamlines equipped
with an in situ microspectrophotometer. When checked, the software
will automatically collect a UV spectrum after a number of frames
entered by the user. The number of frames defaults to the amount
specified by the wedge. The spectrum will always be collected at the
same orientation given by the phi angle selected by the user
(defaults to the data collection start). To calculate the optimal
phi to monitor the spectrum, please refer to the documentation
for the microspec tab.
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Starting a Data Collection Run
- After setting all parameters to your desired values click Start to collect an image.
- The network status of your Blu-Ice Client must be Active to collect an image.
- If you have
created a few runs and start data collection from a previous "run", Blu-Ice will collect frames from the current run and the following runs (Note: Blu-Ice will not recollect frames from an already completed "run"). This allows users to collect multiple data sets (eg., low resolution pass, high resolution pass or different wavelengths) using different "run" windows.
Run Time
- Run Time shows the time remaining for the data collection run. If new values of data collection parameters are entered in the
run definition, the run time is recalculated. During the run, the run time is updated after every image.
Data File Naming
- Each data file in your selected run sequence is named in
the following way: 'file prefix'_'run
number'_'energy number'_'image number'.img.
- For example, a file could be named data_2_E2_010.img. This image is in the
10th frame collected in Run 2 at the 2nd input energy.
- With only one energy level selected, the file would be name 'file prefix'_'run number'_'image number'.img.
Run Sequence
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- The run sequence depends on the values for phi, wedge, energy or
inverse beam that you choose. The image collection
order will be displayed in the 'run sequence'
window. Below are examples of some possible run
sequences.
- Note: Once the current run is finished, the software will go on to
collect any unfinished runs (paused or inactive) following the current one.
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One Energy, Inverse Beam Off, Phi < Wedge Size (simplest case)
test_1_001
test_1_002
test_1_003
(phi: 0-3 deg, wedge: 3 deg, 1 energy, inverse beam off)
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Two or more Energies, Inverse Beam Off, Phi < Wedge Size
example:
test_1_E1_001
test_1_E1_002
test_1_E1_003
test_1_E2_001
test_1_E2_002
test_1_E2_003
(phi: 0-3 deg, wedge: 3 deg, 2 energies, inverse beam off)
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Two or more Energies, Inverse Beam On, Phi < Wedge Size
example:
test_1_E1_001
test_1_E1_002
test_1_E1_003
test_1_E1_181
test_1_E1_182
test_1_E1_183
test_1_E2_001
test_1_E2_002
test_1_E2_003
test_1_E2_181
test_1_E2_182
test_1_E2_183
(phi: 0-3 deg, wedge: 3 deg, 2 energies, inverse beam on)
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Two or more Energies, Inverse Beam On, Phi > Wedge Size
example:
test_1_E1_001
test_1_E1_002
test_1_E1_181
test_1_E1_182
test_1_E2_001
test_1_E2_002
test_1_E2_181
test_1_E2_182
test_1_E1_003
test_1_E1_183
test_1_E2_003
test_1_E2_183
(phi: 0 - 3 deg, wedge: 2 deg, 2 energies, inverse beam on) |
Image display commands
New images are displayed to the left of the collect tab as soon as
they are written to the users' area. Older images can be displayed and
inspected by launching the web-browser based Image Viewer in
Web-Ice or the program ADXV.
brightness
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- The default image Brightness value is set to 400. Change this value for a desirable contrast between spots and background.
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zoom
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- Click on this to zoom in or out of the diffraction image.
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move arrows
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- Pans the image within the display box.
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Alternative image viewers
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- Allows the user to inspect and analyze diffraction images
with Web-Ice or ADXV.
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Select image
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- Allows the user to select the previous and next images in
the run sequence with
the + and - buttons. To use this tool while data collection is
ongoing, click the Hold image check box.
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Useful Tips
- Subdirectories are automatically created.
- The next image to be collected is colored red in the 'Run Sequence' box. You can jump to a different image if you double click on the desired image name.
- Pressing the "Pause" button stops the data
collection after completing the current frame, or, in the case
of shutterless data collection, after completion of the
current wedge. Pressing the "Abort" button immediately stops the data collection.
- Double-clicking on an image automatically starts ADXV.
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