Notable Changes in SerialEM 4.1

11/30/23: DE code and DLL updated to work with 2.7 server; API 2 can now be used with 2.7 but not earlier servers and gives fast continuous mode.

11/14/23: Added option to Tilt Series Extra Output to make a map from a low-tilt Record for each series run from Acquire at Items.

11/2/23: Added options to use Ctfplotter instead of Ctffind for CTF fitting when click in FFT and for coma/astigmatism correction.

10/17/23: Added button in multishot dialog and script command to use the current group of Navigator points to define vectors.

10/12/23: Added automatic pruning of log window.

10/6/23: Added script commands and other functions to control beam stop on newer JEOL scopes and FEI scopes with UTAPI interface.

9/27/23: Added a non-Qt version of Ctfplotter to install package and changed SerialEM to use this unconditionally unless a graph is being saved.

7/12/23: Added buttons to apply an adjustment and to use hole vectors from a map to the multishot setup dialog.

7/10/23: Image shift values corresponding to hole vectors are computed after finding holes on a map and stored in the Navigator file; they can be used later for multishot vectors with a script command.

7/10/23: Shift-middle-double-click near the blue rectangle drawn for a map will make it load that map.

7/5/23: Allowed taking subareas in dose fractionation mode for K2/K3, needs new plugin.

7/3/23: Added entry for extra file suffixes in the Tilt Series Extra Output dialog to replace having to use 'SuffixForExtraFile' command.

7/2/23: Added an AutoIT compiled executable that is used to change aperture size for systems where the UI automation fails to do so (Win 7, some Win 10).

6/21/23: Allowed adding Navigator items on centered cropped image.

6/17/23: Kept track of whether a cropped image was centered and allowed Navigator display on such an image.

5/28/23: Added ability to include a file into a Python script.

4/26/23: Added slider to hole finder dialog to exclude holes near edge of area of found holes.

4/16/23: Added Script menu entry to prevent program from returning keyboard focus to one-line script window.

4/10/23: Added details about shots, remaining numbers, and rates to progress line during Acquire at Items.

3/31/23: One-line script changes: focus now returns to the text box of the script that was run when it finishes. Enabled Ctrl-C and Ctrl-V for copy and paste, Ctrl-U to delete the line, and up and down arrows to move between lines.

3/30/23: Added ability to enter multiple commands separated by semicolons in one-line script window.

3/30/23: Added ability to do alignment correlations after erasing peaks in FFTs from periodic structures; this is used by default for stage and image shift calibrations and in Realign to Item in low dose mode, subject to override by a property, and otherwise controlled by an option in the Image Alignment & Focus panel.

3/9/23: Added capability for "status lines" at the bottom of the Camera & Script control panel that can be written to by script command.

3/1/23: A dashed red rectangle will be drawn when an image extends beyond property-based stage limits.

2/7/23: Used Microsoft "UI Automation" to add aperture support for FEI scopes on Windows 7 or above to retrieve names from the Autoloader panel with ReportSlotStatus.

2/7/23: Added dialog for setting imaging conditions before imposing first image shift in the Step To and Adjust IS procedure for multi-shot setup.

1/29/23: Added option to the multi-hole combiner to remove or turn off combined items with fewer than a selected number of holes.

1/29/23: Added support for grids with hexagonal arrays of holes. Processing is slow, not all optimized, and not in the background - be patient.

1/18/23: When doing multishots in a regular array of holes, the routine will now move to the holes in a spiral path by default, with a menu entry to select the old zigzag path or a raster path instead.

1/16/23:Added option to do a hybrid montage with image shifting within blocks of pieces and stage shifting between the blocks.

1/13/23: Made it possible to set marker point outside image for shifting to marker (shift-P and To Marker button) and Go to Marker in Navigator.

1/4/23: Added a high-defocus image shift calibration, which improves many operations when working with defocused View and Search images.

12/29/22: Made all 5 range-selecting keys in Navigator work with groups collapsed. Allowed easy deletion of multiple maps in a range with Shift D.

12/23/22: Added dialog for autocontouring grid squares and converting selected ones to polygons.

12/16/22: Added dialog to run Coma vs. Image Shift calibration; the positions tested can seen on a View image and distance and rotation of vectors to positions can be adjusted in dialog.

12/15/22: Allowed images from ScaleImage and FilterImage to be made maps, as well as ones resulting from arithmetic operations as long as both contributing images are eligible to be maps.

12/9/22: Incorporated improved montage piece alignment routine recently implemented in IMOD. Added checkbox to Montage Control window to make it evaluate multiple peaks with cross-correlations weighted by deviation from expected shift, which helps when there are regularly spaced holes. Made it use a special set of filter parameters for montages that appear to be for whole grid maps, to prevent correlations dominated by holes. Made correlations run in a background thread while the next piece is acquired, when possible.

11/30/22: Made the Basic Mode filename be saved and loaded from settings, and added a menu entry to load a different file.

11/16/22: Added AutoContourGridSquares command to make polygons around grid squares.

11/16/22: Added ability to have up to 3 more rows of script buttons and spinners in the Camera & Script control panel.

11/10/22: Removed New Map and Delete Item from Navigator menu.

11/8/22: Started saving shifts from Shift to Marker in settings and added a list box to allow removing shifts.

11/7/22: Switched distribution to being built with Visual C++ 2015 tools. SerialEM will no longer run directly on Windows 2000 and XP SP1 or SP2 but has to be run on a separate computer connecting to FEI-SEMserver on the scope computer. A Visual C++ 2015 redistributable package must be installed to run on Windows XP SP 3.

11/1/22: Added task to Acquire at Items to run hole finder and combiner after acquiring a map.

10/27/22: Added false color display with F12 as a hot key and replaced the Autozoom button in the Image Display panel with this.

10/27/22: Added script command to computer ice thickness from energy- filtered/unfiltered pair of images.

9/20/22: Added ability to save Focus and Trial states in Low Dose, and automatically restored prior state when Low Dose is turned on or off.

9/15/22: Added buttons to the multiple Record setup dialog to step to positions in an existing pattern and adjust image shift values, and to use the vectors from the last hole-finding for a regular pattern.

9/15/22: Added File menu entries to close all open files and to specify initial saving and autosaving of the log.

8/24/22: Added ability to run the Ctfplotter program from IMOD instead of the built in Ctffind.

7/19/22: Added ability to toggle drawing of a range of Navigator items with the V key, as for A, D, etc.

5/21/22: Changed "Ask about making map" to "Make map..." in montage setup dialog, so it will no longer ask, just do it as specified.

3/28/22: There can now be up to 100 files open.

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.