Notable Changes in SerialEM 3.7

1/22/19: The one-line script window is now resizable and can contain up to 5 scripts. The window will reopen on program startup if script windows do.

1/22/19: CPU-based frame alignment for K2/K3 is now done through a separate program to solve memory leaks in DM, allow faster FFTs with Intel libraries, and eliminate license issues with using FFTW.

1/8/19: Initial processing steps for frame alignment can now be done on the GPU, which can greatly speed it up for faster cards with enough memory.

1/7/19: Added properties for defining entries in a Tools menu for running external programs, and script commands for running programs similarly.

1/7/19: Added property to specify a possibly multiline title entry to be included in frame files saved from K2/K3 and in frame stack mdoc files.

12/20/18: Added basic support for moving to next phase plate position on FEI scopes.

12/5/18: Made it possible to save unnormalized hardware binned frames from K3 and get a gain reference for normalizing them.

12/2/18: Added option to save an mdoc file along with each frame stack.

11/19/18: Started storing size and position for individual script editors and added an option (defaulted on) for editors to be restored when the program is started or settings are read.

11/5/18: Enabled post-actions for Falcon and DE cameras when aligning frames in SerialEM so tilting can be done before aligning.

11/4/18: Added script command to move phase plate to next position on JEOL, and changed aperture and phase plate movement to be done with a thread.

10/29/18: Added focus, stage, and screen control to scope control panel.

10/21/18: Allowed continuous mode to be used for mag IS offset calibration and enabled everything but mag button in scope control panel during this cal.

10/21/18: In continuous mode, enabled scope control panel and made it blank beam during operations like mag change that make transients.

10/1/18: Added a menu option to add a grid of points just like the last one, without having to answer any queries.

10/1/18: A grid of points can now be specified by 7 points instead of 5 to overcome inaccuracy in the inter-hole interval specified by adjacent point.

10/1/18: Made it possible to set up tilt series or new file at items for a range of points by pressing Shift T or Shift N twice.

10/1/18: Made the first off-center multi-shot image within a hole be taken along the tilt axis.

9/27/18: Added ability to tilt in steps, shutter the beam, and optionally change focus or image shift during an acquisition that saves frames. Added script commands: to set this up for regular tilts or for ones specified in an array variable that can be read from a text file; to save a file with actual tilt angles; to give the K2 camera a threshold below which it will skip saving frames.

8/24/18: Made SerialEMCCD plugin open all TIFF files as big TIFF to be able to save > 4 GB.

8/6/18: Added ability to use Ctrl to extend the delay time for getting a single mag or spot change when using the spinners in the scope control panel.

8/6/18: Made Unblank button in Low Dose and STEM control panels able to blank beam also.

8/3/18: Eliminated Low Dose radio buttons for area to show when screen down.

7/19/18: Added ability to continue script commands onto multiple lines by ending them with a backslash after a space.

7/19/18: Added separate buttons for going to a low dose area to low dose panel and reverted the radio buttons to just controlling show when screen down.

7/2/18: Added a small delay per frame to startup delay in K2 with dose fractionation. Revised camera timing output and instructions to tell people just to use the minimum StartupDelay instead of changing the allowed minimum.

5/29/18: Made beam intensity calibration use counting mode for K2 when dose rate is low enough and set exposure and count parameters automatically.

5/6/18: Made autofocus abort if too many iterations measure a defocus near zero, and if there are too many iterations where the change was not limited.

5/6/18: Made Montage Prescan not increase the binning by more than 2 for some CMOS cameras with fast readouts (direct detectors, OneView, Ceta), and made it not drop the exposure time so much in low dose mode by allowing counts to increase up to 4-fold.

4/27/18: Multiple records can now be taken from multiple holes as well as from multiple positions in a hole.

3/28/18: Added ability to run a script after each acquisition in acquire at items.

3/21/18: Added calibration of beam tilt needed to compensate image shift, made multi-shot routine able to use this, added some related script commands and options on image shift commands to do compensation for the image shift.

3/21/18: Added ability to make a true JPEG file because ImageJ will not display JPEG-compressed TIFFs and made JPEG/JPG an allowed file type on the SaveToOtherFile command.

2/18/18 Added script command that behaves like Echo but evaluates arithmetic expressions.

2/16/18: Arithmetic expressions are now allowed on all script commands starting with "Set" and many others.

2/10/18: Added routines for astigmatism correction and coma-free alignment by CTF fitting to images with Thon rings. The latter is much better than the old coma-free alignment routine and requires no calibration.

1/23/18: Added output on status bar of frequency and resolution for a point clicked in FFT with middle mouse button.

1/23/18: Added ctffind module, options to support fitting to Thon rings when click in FFT, and CtfFind script command to run it with specified parameters.

1/3/18: Added menu option and script command to reduce an image in size with an antialiasing filter.

1/3/18: Added script command to start Navigator Acquire when the script ends, and a Postpone button to the Acquire dialog for setting parameters only.

1/1/18: Added option to save multiple extra Records into separate stack files instead of all into one.

1/1/18: Allowed up to 6 STEM channels to be obtained simultaneously during tilt series. Added STEM channel name to mdoc file.

12/29/17: Made truncation when saving as bytes be expressed as percentage instead of number of pixels, be saved as a setting, and have a separate value for single-file saving so JPEG-compressed TIFFs can look OK without adjusting contrast.

12/18/17: Add frame alignment parameters for binning to a target size to avoid a set binning becoming inappropriate for different size frames.

12/3/17: Added frame alignment for DE camera frames.

11/26/17: Added option to skip file properties dialog. Started saving file type and compression type for save single/other in settings so it would be easy to save a particular type of compressed tiff from that command without having to revisit the file properties dialog.

11/24/17: Made the program store the fraction of the area in the frame occupied by the main image window so that the window can be kept reliably smaller than the frame; the allocation of width between the main and FFT window is also stored and can be easily adjusted.

11/19/17: Added small dialog for entering and running a single-line script command.

11/3/17: Preliminary version with changes for DE camera counting/super-resolution modes and ability to set save folder.

11/3/17: Rearranged camera setup so that dark reference options could be hidden when inappropriate, also hide shuttering and lower size buttons for Falcon.

10/21/17: Added a task to take multiple Record shots in a hole with image shift, a script command to run the task, an option to draw the pattern of shots when showing the Acquire area in Navigator, and a dialog to set the parameters for the task and for drawing.

9/12/17: Added ability to align frames from Falcon cameras in SerialEM and write command files for aligning with IMOD, just as with K2.

8/31/17: Added option to save frame align com files to same folder as frames.

8/28/17: Started using faster Intel FFT routines.

8/8/17: Added ability to set View or Search shift offsets by placing the marker at corresponding points in two images.

8/7/17: Search mode in Low Dose now has almost all the capabilities as View, with the ability to take montages in Search, set defocus and shift offsets for it, and have those offsets used properly in Realign to Item.

8/7/17: Added separate camera parameters for Search, and a new parameter set that can be selected to be used for montages. If fewer options are desired in the camera setup dialog, each of these can be hidden.

7/14/17: Added ability to align subset of frames either in plugin or in IMOD when saving K2 frames.

7/14/17: Added ability to restrict frame alignment parameters to 4K or 8K frames, or to aligning in plugin versus IMOD, with some automatic switching when appropriate.

7/5/17: In Navigator Acquire at Items, added options for doing a subset of items, skipping stage move if possible, and skipping stage move in Z. There is also a script command to enable skipping the stage move.

7/4/17: Added to mdoc file the dose per frame when frames saved, and prior cumulative dose in Record area for tilt series images.

5/17/17: Script processor now searches in current script first for a function with no script name in front of it, thus allowing duplicate function names in other scripts.

4/15/17: Added script command for writing a single-image file of specified type and compression.

4/15/17: Added option for saving TIFF files with JPEG compression.

4/13/17: Added automatic indentation of scripts with Tab/` and stabilized line in editor window when Tab is used.

4/13/17: Changed dose rate output in microscope status panel to be per square Angstrom and appear unconditionally, and changed dose rate output in camera setup dialog to be rate at camera, estimated from prior images.

4/9/17: Added ability to import navigator items with positions defined by image coordinates on maps.

3/8/17: Fixed transformations used in Navigator to account for tilted images; basic navigation, polygon montages, and Realign to Item seem to work.

3/6/17: Implemented use of live mode for continous acquisition from DE cameras and enabled acquisition of normalized images from server.

3/2/17: Added output of aligned piece coordinates in montage overview to mdoc file.

2/26/17: Added script commands to report and set the value of many user settings by the name used in the settings file.

2/26/17: Added Focus menu option to make an array of FFTs of images with beam tilt in 8 different directions (a Zemlin tableau).

2/18/17: Switched to using standard API for Direct Electron camera instead of COM interface. To use a DE camera, a small plugin, DEcamPlugin.dll, and the interface library, DeInterface.Win32.dll, must be put in the directory with SerialEM, but these are not required to run the program.