Notable Changes in SerialEM 4.0

2/24/22: Changed RotationAndFlip value in .pcm files when aligning in IMOD to -2, so that if nonnormalized files saved without reorientation are aligned in IMOD 4.12.18 or higher, it will reorient the aligned sums properly.

2/24/22: Sped up variable frame summing in SEMCCD plugin when saving unnormalized frames.

2/24/22: JEOL scopes with original defaults for image shift delays will have ISDelayScalingFactor set to 0.2 based on new measurements.

2/22/22: Made it possible to avoid making a temporary stack when doing K2/K3 early returns; early return will now show some or more benefit when using it for multiple Records.

2/22/22: For Titan or scopes with Advanced Scripting, the program will adjust image shift settling times to new, much lower values if ImageShiftDelays are still at the original defaults and ISDelayScaleFactor is not set.

2/22/22: Fixed parsing of /*/ comments in properties file.

2/22/22: The tilt delay set in the tilt series setup dialog is now separate from the general tilt delay which applies during eucentricity.

2/22/22: Added option to iterate beam autocentering.

2/17/22: Increased available number of scripts to 60.

2/16/22: Made alignment in DM with a K3 use the MotionCor2 capability.

2/16/22: Made Zemlin tableau use Record images with CTF acquire parameters.

2/9/22: Made it possible to see Record/Focus areas on all acquire points by turning on Show acquire in Edit Focus mode.

2/7/22: Added script commands to scale an image to bytes, paste two images side by side or vertically, produce a reduced spectrum scaled to bytes, and produce a side-by-side reduced image and scaled spectrum.

2/7/22: Added button to save Mont-map states, ones having Mont-map instead of Record camera parameters, to the State dialog.

2/4/22: Moved menu entry for setting email address from Tilt Series to Settings menu.

2/1/22: Added option to beam autocentering to use current Trial parameters with a specified reduction in beam size.

1/26/22: Released plugin/server in which saving frames from Ceta 2 works.

1/26/22: Added Navigator Edit Mode feature for selecting multiple points by holding down Ctrl and the left button and moving the mouse of over points.

1/25/22: Added rotation and flip value for K2/K3 to mdoc and made frame files saved without rotation/flip indicate the value needed with "nrf" (which became "need" later).

1/25/22: Made rough eucentricity use previous image instead of original one as reference if shift is big enough, since correlating with progressively larger shifts is more prone to fail. Added script commands to set a limit for Z movement and to test if last run failed due to the limit.

1/25/22: Changed "To file" spinner in Buffer Control panel to a combo box for showing and selecting the current file; kept open files in order in title bar.

1/20/22: Made most tasks taking lower-magnification tracking shots use Search instead of View in Low Dose mode if View has an inadequate field of view but Search has a better one and is not in LM. There is a special option to override this behavior.

1/13/22: Extended autoloader script commands to support the JEOL autoloader.

12/24/21: Made scroll wheel zoom image only when over the image window and scroll either the log or the Navigator table when it is over those windows.

12/19/21: Upgraded state dialog and state saving so that Record, View, and Search states can all be saved and set, including focus offsets, and so that target defocus can be saved outside of Low Dose mode.

12/19/21: Added support in SerialEM for saving and aligning frames from Ceta 2 camera (plugin not finished).

11/23/21: Changed from two primary actions for saving images in Acquire at Items to one action with a checkbox for making a map. Also allowed this action to be with View/Search images regardless of whether a map is being made.

11/16/21: Enabled buttons for defining Trial/Focus areas in Search mode.

11/2/21: Made hole finder check spacing between holes with analysis of autocorrelation peaks using pixel size routine.

11/2/21: Added option to Acquire at Items to take single-image maps in Low Dose with View or Search.

10/27/21: Allowed / ... */ comments in scripts

10/25/21: Added support for getting refrigerant level and time remaining until a refill from JEOL scopes.

10/12/21: Changed terminology for dose rate from "unbinned pixel" to "physical pixel".

10/6/21: Added commands to do an autofocus calibration over a wider range with measurements at a sparse interval outside the normal range; increased limit on number of points in a focus calibration.

10/6/21: Allowed / */ to enclose multiline comments in properties file.

8/23/21: Changed multi-hole combiner to use image positions for a montage whenever possible (i.e., if points were drawn on a loaded map), which fixes problem of bad center positions when there are big piece offsets.

8/17/21: Put stage coordinates of marker point in status bar when Navigator is open.

8/4/21: Expanded the set of tasks that Navigator Acquire at Items can run, provided flexibility in where and when they run, added multiple Records as another primary acquisition action, revamped the Acquire at Items dialog and made it nonmodal so other setup dialogs can be opened and checked from it, and added various other options that should allow SPA acquisition to be done without scripts.

8/4/21: Added routine for managing nitrogen filling and vacuum pump events and a dialog for setting parameters.

8/4/21: Added routine for aligning to a template image, which is saved as a map and has to look like a cropped image.

6/29/21: Added routine to set eucentricity by measuring defocus.

6/22/21: Added ability to use "Shift to Marker" on mag-specific subsets of items and to save shifts for reuse on newly acquired maps.

6/15:21: To allow extra tilt series output settings to be varied in batch acquisitions, added a button to open the extra output dialog to the tilt series setup dialog when it is opened from Navigator.

6/12/21: Added support for FEI Selectris filter.

5/5/21: Added ability to embed Python inside regular scripts.

4/29/21: Allowed a regular script function to be called from Python, switched to collecting standard output from Python and putting it in the log so that the standard 'print' function could be used.

4/28/21: Allowed a regular script to be called from a Python script, and a Python script to be called from a regular script. Added ability to return values from a function or script call with the Return command.

4/23/21: Changed Python scripting to run Python executable with script to solve import problems; this also allows external control from a Python script. Added a command to place an image into a buffer.

3/31/21: Added ability to use a monospaced font and to adjust indentation more easily in script editor.

3/23/21: Python scripting now works, with plugins available.

2/22/21: Added options to use Search area to Autofocus script command.

2/16/21: Made excluded points in the hole finder be colored light or dark blue depending on which mean cutoff they exceeded.

1/10/21: Expanded ability to hide dialog elements and made it possible to close up empty space in control panels after hiding.

12/27/20: Added ability to do rough eucentricity with Search area.

12/16/20: Moved slow lens changes with normalizations into threads so that the user interface stays responsive during long changes.

12/15/20: Added option to draw tilt axis to Image Display panel and added a tilt axis line on View/Search images when defining Trial/Focus areas.

11/24/20: Added support for HDF files.

11/10/20: Added capability to define dialog and menu items to hide or disable unconditionally and also to define a selectable "basic mode" with a list of items to hide or disable.

11/2/20: Changed cosine power specification in the tilt series setup dialog to be expressed in terms of increase in exposure from 0 to 60 degrees.

10/4/20: Enabled display of Low Dose areas on Search images.