Leginon

h1. Leginon System version 1.6

Version 1.6 contains enhancement that is not available in version 1.5 and release of a

series of Robot Screening application. Most significant changes are the split of Drift Manager

functions to Transform Manager which handles the transformation of targets using any level of

ancestry rather than one in the original Drift Manager. This allows an expansion of method that

is meant to improve targeting accuracy. There are also significant improvement in Tomography

node and its operation.

# [[pyScope Change]]

# [[New User Features]]

# [[Updated Applications (All)]]

# [[New Project Web Tool Features]]

# [[New dbemtool Web Tool Features (1.5.1)]]

# [[Bug Fixes]]

# [[Recommended Application Preference Changes when updated from version 1.5]]

# [[Known Bugs]]

h2. pyScope Change

With increasing number of instrument conflict, a configuration file is now required to

specify the instrument available on a host.

h2. New User Features

h2. General

* The settings window gui can all fit in 12" laptop display now

h2. Acquisition/Navigator Class

The following applies to an acquisition node that uses the navigator to move to its

target:

*  Based on a threshold, Targets can either be aborted or forced to collect when the

multiple move failed to reduce further before reaching the goal.

*  It is possible to improve the targeting accuracy with a combination of stage

movement and final image shift. However, this requires specific relationship between

the acquiring presets and parent image presets. It works currently only for tomography

and depth-first traversal MSI scheme.

h2. BeamFixer Class (New)

Simple beam shift adjustment to correct unstable beam position in long runs.

h2. BeamTiltImager Class (New)

Visual aid to coma-tilt alignment. It is used to acquire images of beam tilt

difractogram tableau. The user can then click at the location of the tableau where he/she

considers as the coma-free and therefore adjust the beam tilt. See Node Description Chapter

for details.

h2. Corrector Class

* A bad pixel region can be specified by clicking the corners and added to the bad

pixel plan

* Extreme intensity pixels can be found by a click on this tool!http://emg.nysbc.org/software/leginon/images/icons/stagelocations.png!

* Normalization image of the chosen camera configuration can be displayed.

h2. DriftManager Class

* A timeout for drift monitoring can now be specified so that if the drift is

incorrectly detected due to an empty imaging area, the acquisition of the target will

be aborted.

h2. DTFinder Class (New)

Dynamic template finder is developed for tissue section imaging. An initial template is

defined by the user. The subsequent images it receives are then shifted and rotated against

the template to find the best match to the section so that the target selected on the

template can be transferred on to the new image.

h2. FFTMaker Class

* Power Spectrum is displayed if processed.

* Option for calculating power spectrum but not saved to disk.

* Option for calculate a truncated power spectrum to speed up the calculation for

large images.

h2. GridEntry Class (New)

Direct entry of grid information to Leginon database to organize the data acquired. The

main use is for simple one-pass grid screening of multiple grids when the robot does not

exist.

h2. ImageProcessor Class (New)

Base class for process images of a completed image target list. Mainly used for

development of batch processing of the images acquired such as image stack creation of a

tilt series. An example of its use is in filenames.py.

h2. ManualAcquisition Class

* The acquired image can be sent to FFTMaker.

h2. PresetsManager Class

* Preset Beam Ajustment Tool allows easier semi-automated adjustment of multiple

presets at the same magnification.

h2. PixelSizeCalibrator Class

* Power spectrum calculated from acquired image is displayed.

* Distances measured between diffraction spots are used for an user-interactive

pixel size calculation and averaging.

h2. Robot2 Class (Replacing Robot)

This class replaces Robot Class in all applications. It commnunicates to grid handling

robot(s) through database. A few default settings are changed to reflect it and also the

more general usage

* Simulate Robot Insert/extraction = True

* Default Z Position = 0

h2. TargetFilter Class

* The images and targets that are filtered are displayed.

* User inspection and editing of the filtered targets are allowed.

h2. Tomography Class

* Allow the model to remain fixed to the initial values.

* Separate goniometer models for positive and negative tilts.

* Options that are not found useful are removed.

h2. TransformManager Class (New)

This class will eventually handle the transformation of an old target to a new one for

reacquisition after shift, tilt, and/or rotation in the grid plane. The current use is to

replace the shift adjustment in Drift Manager. As an option, it can transform targets based

on more than just its parent but all direct ancestors which makes the range of shift it can

handle much larger than the original drift manager implementation.

h2. Updated Applications (All)

h2. Manual

Power spectrum can be automatically calucated from the acquired image and displayed in

its own node to allow easy inspection.

h2. Calibrations

New binding required by Navigation node.

h2. MSI

New binding required by Navigation node. Drift management is divided between Drift

Monitor and Target Adjustment. A Preview and a Beam Fixing node are now standard in all MSI

applications

h2. Robot-related applications

Robot2 class that uses database as midpoint to communicate bettween leginon and the

robot controller replaces Robot class

h2. New Project Web Tool Features

h2. Grid entry for Robot Trays (1.1)

This is used to enter grid information for robot trays.

h2. Appion processing database creation (1.2)

This is used to create and link the project to a new database ready for Appion usage.

h2. New dbemtool Web Tool Features (1.5.1)

h2. Hide or exemplify an image in the viewers

Images can be one of the three status: Normal, Hidden, or Exemplar. Clicking on the hide

button above the displayed image where it is available moves the image from its current

list. In other words, to hide an image from any of the normal preset list, click on "hide"

while display a normal image. This image will now display only if "hidden" is selected from

the preset list. Clicking on "hide" above an image displayed in the hidden list removes it

from the "hidden" list and return it back to the normal list. Images put in the "exemplar"

list will also be shown in the normal list.

h2. The mrc images are cached as jpegs in the viewers

The cache system allows faster access to the same image next time.

h2. More options for image display intensity adjustment

You can manually define min/max of the display range in absolute number or relative

percentage, as well as in standard deviation unit based on the statistics of the image. The

manually determined values are saved for individual image displayed in the same panel until

the page is closed.

h2. Queue counter in LOI

It updates the number of unprocessed queue targets and estimate how much time it will

still take to finish them.

h2. Queue deletion tool in 3-way and LOI viewers

Click on this tool<inlinegraphic

fileref="http://emg.nysbc.org/software/leginon/images/images/deq_bt_off.gif"

format="GIF"/> above a displayed image pops up a window where you can remove targets

derived from that and all its descendent images. In other words. if you have put in the

queue targets from 10 holes, each selected from the same square image, you will delete all

theses targets if you perform queue deletion on the square image. Please use this

carefully.

h2. Hole template and 2-way viewers

You can see your custom hole templates saved and used in the past leginon sessions in

the hole template viewer. 2-way viewer gives you a bigger view of the parent images than the

3-way viewer.

h2. Model parameter display in the tomography viewer

The model paramters can be displayed for diagnosis by activating the check box.

h2. Deletion candidate marking in the tomography viewer

The "Mark for deletion" button saves the selected tilt series in the leginon database in

a table that the system administrator can look up and delete from the file server in a later

time.

h2. Appion processing function possible with installation

If you install Appion's processing server programs, the processing tag direct you to its

menu page.

h2. Bug Fixes

h2. GUI

* Tomography node settings is set in a scrolled window so that it is possible to fit

it in a smaller display such as 12" screen of laptop computers

* Goniometer Modeler settings are automatically set.

.

h2. Recommended Application Preference Changes when updated from version 1.5

h2. Adjust Target For Drift Check Box is now a choice

If you checked "adjust target for drift" in any node of Acquisition class, it should be

changed to select "one" ancestor. A python script "update16.py" is provided for a complete

update of such setting in all related nodes. If the drift is so large that the different

versions of the parent images can not be correlated, you should change the choice from "one"

to "all" ancestors.

h2. Known Bugs

* (New for v1.5) Resuming image acquisition from Square Targeting after Leginon

restart may cause reacquisition of children of the unfinished target list on 32-bit

Linux machine.

Dictionary ordering problem of MySQL query, No temporary solution.

* (New for v1.5) DataAccessError may show up when a user starts new application if

default is loaded to an existing database.

Temporary solution: See <link linkend="bad_default_reference">Operation Trouble

Shooting</link> on the subject.

* (New for 1.3) Navigator multiple move option does not work properly in MSI imaging

sequence with image shift as the move type.

Temporary solution: Always use preset manager when move type is image shift.

* Web viewer may not display all targets on the parent image since target is

transferred to a different version.

No temporary solution.

* Kill Application may not kill all process cleanly and may cause problem in

connecting to TEM or camera when a new application is reloaded.

Temporary solution: Close leginon and clients and restart.

* Simulate Target use the current image shift as the target shift on top of its preset

shift. Therefore, the acquired image may carry an additional image shift if there is an

offset created from previouis acquisition.

Temporary solution: Always use Presets Manager to send the preset to be used in

simulation first before usinging Simulate Targets tool.

* Some, although fewer, User Notification "processing " icons do not disappear but

stay pointing up after the node is done.

Temporary solution: None.

* When running on LINUX system, Preset selection in /Presets Manager/Importing Presets

from Another Session/ add a selection when mouse is left-clicked rather than toggle the

selection as in convention.

Temporary solution: Hold down to Ctrl key to select and deselect multiple presets.

Shift key still means selecting all between the two clicks.

Note: This problem is caused by some bug in wxPython for LINUX.

* Web 3way Image viewer does not always show in yellow the revised (i.e. after drift

correction) current target in the parent image.

Temporary solution: None.

* Starting Manual Focus directly by clicking on the tool does not use preset but still

check for the preset assigned for the focuser node.