1) A bug was fixed that caused the Project command in V1.56 to fail when attempting to do mean value projection.
2) A bug was fixed that caused the brush and eraser tools in V1.56 to be offset one pixel down and to the right.
3) A bug was fixed that caused the Register command in the V1.56 (PPC version only) to fail.
4) A bug was fixed in the SetThreshold() macro command that prevented macros that continually adjusted the threshold under keyboard or mouse control from working correctly.
5) The Undo macro command now works with Paste.
6) Max Particles in the Analyze Particles dialog box can now be set to a value greater than 999,999.
7) A bug was fixed that sometimes caused color TIFF files to be written with a corrupted color table if the monitor was not in 256 color mode.
8) NIH Image now opens most uncompressed 24-bit (RGB) TIFF files. Like the Acquire and Capture Color commands, the images are loaded into a 3-slice stack.
9) The DICOM import routine (new in V1.56) was improved. In addition to DICOM-3 images, it now reads many ACR/NEMA images. It now requires a DICOM dictionary to decode the DICOM or ACR/NEMA header. The dictionary is available from zippy.nimh.nih.gov, in the /pub/nih-image/documents directory. It must be located in the same folder as NIH Image or in the System folder. Hold the option key down to get a full dump of the DICOM header. Hold the shift key down to fix the 16-bit to 8-bit scaling when using the "Open All" option.
V1.56 Release Notes (20 Dec 1994)
-------------------------------------------------
1) A bug was fixed that caused the SurfacePlot macro command to fail when generating grayscale/color surface plots.
2) A bug was fixed that sometimes caused diagonal lines to appear when using the Revert to Saved command with odd-width TIFF files created by programs other than NIH Image.
3) A bug was fixed that caused images imported with "Invert" checked to be inverted by the Revert to Saved command.
4) A bug in the "Gel Plotting Macros" was fixed that could cause incorrect results if the foreground color was not black (255).
5) The Capture Frames shutter click sound that was missing in V1.55 is back again.
6) A new macro package ("Markup Macros") was developed that enables objects in an image to be outlined and labeled and the resulting graphics and text saved as a separate file.
7) The "Halftone Options" command was removed from the File menu and the "Custom Grayscale Halftoning" check box was removed from the Preferences dialog box. The custom halftoning dialog box is now accessed by holding down the option key while selecting the Page Setup command.
8) A bug was fixed that sometimes caused a crash when using the "Uncalibrated OD" option in the Calibrate command.
9) NIH was ported to the PowerPC using the Metrowerks PPC Pascal compiler.
10) A bug was fixed that caused the 'max' value returned by the GetPlotData macro routine to always be zero when all of the Y values where less than zero.
11) The spray can tool now works at slower speeds on faster macs.
12) Interactive editing of the Map (by holding the option key down) now works when the monitor is not in 256 color mode.
13) Images captured with with "Highlight Saturated Pixels" selected are now displayed correctly on monitors that are not in the 256 color mode.
14) Enhance Contrast now works correctly when the monitor is not in 256 color mode.
15) The SaveState and RestoreState macro routines now save and restore text attributes such as type face, size and style.
16) Extra header data are no longer appended to the end of stacks exported as raw data.
17) A bug was fixed in the OpenSerial macro routine that caused even parity to always be used if seven data bits was specified.
18) The angle in the file names of projections saved to disk now have leading spaces so the file names sort correctly by name.
19) "Trace Edges", renamed "Find Edges", now implements a 3x3 Sobel edge detection operation.
20) The Shadow command now allows the user to specify the direction of the simulated light source. The Shadow macro command was modified to accept an optional string argument in the form Shadow(direction), where direction is equal to 'N', 'NE', 'E', 'SE', 'S', 'SW', 'W' or 'NW'.
21) A measurement bug was fixed that caused the standard deviation to be set to zero whenever the mean was less than zero.
22) A bug was fixed that caused the AutoOutline macro command to fail to save the XY coordinates if the wand tool was not selected.
23) The SetScale macro command now accepts an optional third argument that sets the pixel aspect ratio. Similarly, GetScale returns the pixel aspect ratio in an optional third argument.
24) The New and Duplicate commands no longer force the width of newly created images to be even.
25) The result argument in the ImageMath macro command can now be either a string or a pid number. If it's a string, a window with that name is created to store the result, otherwise the result is stored in the image specified by the pid number. Note that the result pid number can be the same as either of the source pid numbers.
26) Support was added for the Scion AG-5 frame grabber. All capabilities of the Scion LG-3 are available with the AG-5 except for digital and analog I/O. The Average Frames command supports the AG-5's ability to do video rate averaging and integration.
27) A check box ("Integrate On-chip") was added to the Average Frames dialog box. This option allows the Scion LG-3 to control on-chip integration using the Cohu 4910 series cameras and modified versions of the Dage-MTI CCD72. When this box is checked, the camera will integrate on-chip for the specified number of frames; the LG-3 will then capture the integrated frame. On-chip integration requires a special cable available from Scion for connecting the integration input of the camera to the LG-3. The string "on-chip" was added to the AverageFrames macro command.
28) Macros (in the "Video" macro file) were developed to continuously integrate and display frames either off-chip, using the Scion AG-5, or on-clip, using the Scion LG-3 and a Coho 4910 series camera. Instructions for using these macro are in the macro file.
29) Density and spatial calibration defined by the Calibrate and Set Scale commands is now "stickier". Before, if you calibated an image and then closed that image, any new images created using the New command would be uncalibrated. Now, in the same situation, the new images will be calibrated.
30) A bug was fixed that caused inverted profile plots to be displayed incorrectly.
31) A macro command was added for specifying what gets saved by the SaveAs command. It has the form SetSaveAs('mode'), where 'mode' is one of: 'TIFF', 'PICT', 'MacPaint', 'PICS', 'LUT' or 'Outline'.
32) The Image Math command now ignores selections. The arithmetic operation is performed in the upper left corner of each image using the largest common rectangle.
33) The settings file ("Image Prefs") is now saved in the Preferences folder.
34) Folder paths such as 'hd400:textfiles:text' can now be used with the SaveAs command when saving the contents of text windows.
35) The name of the macro routine for calling filter plug-ins was changed from 'Filter' to 'CallFilter'.
36) A new macro routine was added for using built-in filters. It has the form "Filter(name)", where name is one of the following: 'smooth', 'smooth more', 'sharpen', 'sharpen more', 'find edges' (or 'sobel'), 'median', 'max', 'min' or 'dither'.
37) A new macro was added for doing density calibration. It has the form "Calibrate('fit', 'unit', m1, k1, m2, k2, ...)", where 'fit' is one of 'straight', 'poly2', 'poly3', 'poly4', 'exp', 'power', 'log', 'rodbard', 'uncalibrated' or 'uncalibrated od', 'unit' is the unit of measurement, m1, m2, etc. are the measured values and k1, k2, etc. are the known values. For example, "Calibrate('Straight', 'Invert', 0, 255, 255, 0)" sets up a simple inverting function. Use "Calibrate('Uncalibrated OD')" to enable uncalibrated OD and "Calibrate('Uncalibrated')" to disable calibration.
38) The Make Montage command now optionally draws borders. The width of the borders can be varied by clicking on the lines at the bottom of the Tools window.
39) The Import command now as an option to import files in the DICOM (Digital Imaging and Communications in Medicine) format used in radiology.
40) The Image Math command can now perform arithmetic operations on density calibrated images and produce a density calibrated result. For example, adding two imported 16-bit MRI images with calibrated pixels values in the range 0-1000 now results in an image with calibrated pixel values in the range 0-2000. Previous versions of Image Math ignored density calibration and always operated on the raw 8-bit pixels.
41) The "Copy Function to LUT" checkbox was removed from the Calibrate dialog box and a macro that performs this function was added to the "LUT Macros" macro file.
42) The wand tool, when used to outline rectangular objects, now creates selections that the Save As command recognizes as rectangular.
43) The "Invert Pixel Values" checkbox in Preferences now applies to all open images not just the currently active image.
44) A macro routine, CallExport('name'), was added for calling export plug-ins.
45) A bug was fixed that sometimes caused NIH Image to hang when using Analyze Particles on an image with one or more very large particles.
46) The Measure command now sets the major and minor axes lengths to zero for spatially calibrated images with a pixel aspect ration not equal to one. In previous versions, the major and minor axes lengths were incorrect if the pixel aspect ratio was not one.
47) The "MCID" option was removed from the Import dialog box and a macro for importing MCID files was added to the "Input/Output" macro file.
48) The Select All and Show Clipboard commands now work with text windows.
49) A boolean function was added to the macro language for checking the state of keyboard modifier keys. It has the form "KeyDown(key)", where key is one of the following: 'option', 'shift', or 'control'. It returns TRUE if the specified key is down.
V1.55 Release Notes (3 May 1994)
------------------------------------------------
1) The PasteLive macro command now works with Paste Control.
2) The Find command will now move the cursor to a specified line in a text window if you enter a search string in the form ‘#n’, where n in a line number. As an example, to go to line 100, enter ‘#100’.
3) Load Macros error messages now display the line in the macro file that caused the error.
4) Routines were added to the macro language for getting the length of a string and for deleting a substring of specified length. The length function (“i:=Length(str)”) returns the length of str. The delete procedure ( “Delete(str,index,count)”) removes count characters from str, beginning at index.
5) A bug (introduced in v1.54) was fixed that could sometimes cause images uncalibrated in the Set Scale dialog box and saved to revert to being calibrated (to pixels) when reopened.
6) A bug was fixed that caused the macro interpreter to fail to skip over string assignments used in IF or IF THEN ELSE statements.
7) The LUT tool now moves one level wide density slices if you click directly on them in the LUT window.
8) A bug was fixed that sometimes caused Plot Profile and Reslice to not work correctly for line selections extending past the image boundary.
9) A new macro command was added that returns the current spatial scale. It has the form “GetScale(scale,unit)”, where scale (real) is the number of pixels per unit and unit (a string variable) is the measurement unit. For uncalibrated images, scale is set to 1 and unit to ‘pixel’.
10) There is now a macro command (“AutoOutline(x,y)”) that is equivalent to clicking with the wand tool at location (x,y). The outline was successfully created if GetRoi returns a width greater than zero.
11) The Dither command no longer ignores pixels along the edge of the image.
12) The SaveAs and Export macro commands now accept full path names. For example, to save the current image in the folder “Images” on the disk named “hd400” use SaveAs(‘hd400:images:myimage’).
13) A bug was fixed that caused all the slices except the first to be inverted when importing multi-slice 16-bit images.
14) The Open command now recognizes and opens imported TIFF files of type ‘TEXT’. Hold down the option key to display the first 32K of the file as ASCII text.
15) The Cancel button in the Rotate Left and Rotate Right dialog box now works.
16) A bug was fixed that caused the “24-bit to 8-bit Color” command to fail with images wider than 2047 pixels.
17) NIH Image now works on grayscale Powerbooks. In fact, it runs with the monitor set to anything from “Black & White” to “Millions”. For best performance, however, 256 colors (or grays) should be used whenever possible.
18) The Save Screen command was removed from the File Menu. Use System 7’s built-in screen dump FKEY (command-shift-3) instead.
19) A bug was fixed that sometimes caused calibrated density values to be incorrect for images opened and processed using a macro.
20) A bug was fixed that sometimes caused “Plug-in Digitizer”, and possibly other acquisition plug-ins, to generate blank images when memory was low.
21) A bug was fixed that sometimes caused enlarged and misplaced text to be displayed in the Image Math dialog box.
22) A new command (Register) was added to the Stacks menu that will translate and rotate the slices in a stack into alignment based on fiducial points. It was written by Michael Castle (mike.castle@med.umich.edu) of the University of Michigan Mental Health Research Institute (MHRI). An example stack and set of fiducial points ("RegistrationExample.bin") are available by anonymous FTP from zippy.nimh.nih.gov in the /pub/nih-image/stacks directory.
23) The Scale and Rotate command now rotates images up to ten times faster.
24) The "Values" window was renamed "Info".
25) The maximum stack size was increased from 256 to 1000 slices.
26) A new option was added to the Surface Plot command to create grayscale or color 3D surface plots similar to the default "wireframe" plots except that the active color LUT is applied to the z-axis of the plot. The code for doing this was contributed by Norbert Vischer (norbert@mc.bio.uva.nl).
27) A bug was fixed that could a crash when attempting to open a window and not enough memory was available. Crashes were most likely to occur when using the "Modern Memory Manager" available on PowerPC Macs.
28) A bug was fixed that sometimes caused stacks to be partially opened without an error message being displayed.
V1.54 (1 Feb 1994)
1) A bug was fixed that could cause the Import macro command to fail when using the “Import All” mode if Import had been previously called in the macro.
2) The Set Scale command now allows the user to enter an arbitrary unit of measurement.
3) A plug-in (“Plug-in Digitizer”), written by Cyrus Daboo of Cambridge University, now allows NIH Image to grab images using the frame grabber built into the AV Macs or from any other Quicktime compatible digitiser with a 'vdig' component. It is available as a binhexed. self-extracting archive by anonymous FTP from zippy.nimh.nih.gov, in the /pub/nih-image/plug-ins directory. The archive also includes a report on the AV digitizer that points out some its flaws, such as automatic gain control that can't be disabled. It also includes Apple's “AV Digitizer Options” extension that allows the user to switch the AV digitizer into grayscale mode, which greatly improves the quality of images captured using grayscale cameras.
4) A bug (new in V1.53) was fixed that caused perimeter and freehand length measurements to be incorrect for spatially calibrated images.
V1.53
1) A command (Project) was added to the macro language for doing projections. The Project dialog box is displayed only one time (the first time Project is called) within a macro.
2) A string function (WindowTitle) that returns the title of the active window was added to the macro language.
3) A bug was fixed that caused Image to display an invalid error message when attempting to open 16-bit TIFF files with contiguous strips.
4) A bug was fixed that could sometimes cause Image to crash when printing, particularly when using a macro.
5) A bug was fixed that caused Image to fail to open some TIFF files created by “little-endian” systems such as the IBM PC.
6) A bug was fixed that caused the Reslice command to fail when the slice spacing was less than one.
7) The NewTextWindow macro command now accepts optional arguments for specifying the text window size and the Dispose macro command now works with text windows. These changes make it easy to write macros that do inline convolutions, for example,
macro 'Sharpen [F]';
begin
NewTextWindow('3x3 sharpen',120,120);
writeln('-1 -1 -1');
writeln('-1 9 -1');
writeln('-1 -1 -1');
Convolve('');
Dispose;
end;
8) A bug was fixed that caused the Plot Profile command to work incorrectly when using a line selection transferred to another image using the Restore Selection command.
9) A bug was fixed that sometimes caused Image to hang when using the wand tool with black backgrounds.
10) The Preferences command can now be used to specify the four character creator code Image uses for exported text files. This code determines which application is launched when you double-click on an exported text file (e.g., measurements, profile plot data, XY coordinates). Use ‘Imag’ for Image, ‘XCEL’ for Excel and ‘QKPT’ for KaleidaGraph.
11) A new command named “Image Math” was added to the Enhance menu for performing arithmetic and logical operations between two images. The corresponding macro command has the form “ImageMath(‘op’, pic1, pic2, scale, offset, ’ Result’)”. The ‘op’ string should be set to ‘add’, ‘sub’, ‘mul’, ‘div’, ‘and’, ‘or’, ‘xor’, ‘min’, ‘max’ or ‘copy’. Pic1 and pic2 are pic numbers or pid numbers. For each pixel in the selection, the specified operation is performed, the result is multiplied by ‘scale’ and then ‘offset’ is added. ‘Result’ is the name used for the window created to store the results. For example, to average two images you could use the command: ImageMath(‘add’, 1, 2, 0.5, 0, ‘Average’).
12) When using acquisition plug-ins, Image now uses the window name specified by the plug-in instead of always using ‘Untitled’.
13) A bug was fixed that caused the Results window to sometimes not be correctly updated when using overlapping windows.
14) The MoveWindow macro command now works with text windows.
15) The SetThresold and AutoThresold macro commands no longer cause the LUT tool to be selected.
16) Image now displays the PrintDialog box when images are selected and printed using the Finder’s Print command.
17) The macro interpreter is now more likely to correctly handle nested IF, FOR, WHILE and REPEAT statements without the need to use BEGIN-END brackets. The interpreter also now requires semicolons between statements.
18) A bug was fixed that caused plug-ins with ‘(‘, ‘/’ or ‘;’ in their names to not be listed correctly in the appropriate plug-in submenu.
19) A new command (PasteLive) was added to the macro language that does a “Live” paste into a selection in a window other than the Camera window. This new command is useful for making montages of different focal planes of fluorescent specimens. Use the “Paste Averaged” macro command in “Video” to do frame averaging of the selection.
20) Image now does a 3-point running average of the XY coordinates to more accurately estimate perimeters of freehand selections and lengths of freehand line selections. Measured freehand perimeters and lengths are now about 10% lower than before. Perimeters reported by Analyze Particles and the wand tool are now slightly lower (2-3%) than those reported by previous versions of Image since they are calculated using this new smoothing routine.
21) A bug was fixed that caused text in text windows to be displayed larger than expected.
22) The Average Frames command now allows you to specify the min and max values that control how integrated images are linearly scaled from 16-bits to 8-bits. The actual 16-bit min and max are always displayed in the Values menu. There is also a new option that creates a calibration function for displaying approximations of the integrated 16-bit values.
23) A Boolean function (PidExists) was added to the macro language for testing the validity of PidNumbers.
24) The “Invert LUT”, “Set Number of Colors” and “Set Extra Colors” commands in the Options menu were combined into a single command called “Lut Options...”.
25) The Analyze Particles command now displays a dialog box with particle analysis options that were previously in the Options dialog box. You can bypass this dialog box by holding down the option key or by using the AnalyzeParticles macro command.
26) A bug was fixed that could cause profile plots of rectangular selections in density calibrated images to be incorrect.
27) A command was added to the macro language for making profile plot data available to macro routines. It has the form “GetPlotData(count,ppv,min,max)”, where count is the number of values, ppv is the number of pixels averaged for each value, and min and max are the minimum and maximum values. The plot data values are returned in a built-in real array named PlotData, which uses indexes in the range 0-4095. The macro “Plot Profile” in “Plotting Macros” illustrates how to use GetPlotData and PlotData.
28) The Gel Plotting macros now work with vertical lanes, no longer require all other windows be closed, do a better job of scaling the lane plots, and report results in calibrated units such as integrated OD.
29) The SaveAs macro command will now save the contents of text windows.
30) The Save, SaveAs, Close and Dispose macro commands no longer require an image be open to work with text windows.
31) The Close macro command now works with the Plot, Histogram, Results, and Video Control windows.
32) The “Import FITS” macro in “Input/Output Macros” now imports both 8 and 16-bit FITS images. It also correctly handles FITS files with headers longer than 36 lines. There is also a new macro for displaying FITS headers.
33) A new string search function was added to the macro language. It has the form “index:=pos(substr,str)”. It searches for ‘substr’ within ‘str’ and returns an integer that is the index of the first character of substr within str, or zero if ‘substr’ is not found.
34) Area and line selection can now be created more precisely on magnified images.
V1.52 (9 September 1993)
1) A bug was fixed that could cause Image to crash when opening text files with names containing a semicolon.
2) A bug was fixed that caused plug-in filters to not work correctly with rectangular selections.
3) Images are now marked as changed when you use a plug-in filter.
4) A bug was fixed that would sometimes cause the Windows menu to become messed up when one or more text windows were open.
5) The window title bar is now correctly updated after a TIFF file has been saved using a new name.
6) The Reduce Noise filter is now four times faster due to some in-line 68000 code contributed by Edward J. Huff at the NYU Chemistry Department.
7) A bug was fixed that prevented filter plug-ins from remembering their settings between calls. You can now also pass the string ‘Reset’ to the Filter macro routine (e.g., Filter(‘Reset’)) to force the next filter called to use its default settings and to display its dialog box, if any.
8) A macro (“Make Expression Movie” in the file “Animation”) was written for generating movies using the Expression plug-in filter. Expression is a freeware program written by Jim Bumgardner (jbum@aol.com) that creates images that change over time according to a mathematical formula. Expression 3.0b, available in the plug-ins directory on zippy.nimh.nih.gov, is required for use with NIH Image.
9) A bug was fixed that prevented selection of the right column or bottom row when using the rectangle selection tool.
10) Thanks to Edward J. Huff, text files created by NIH Image (e.g., macros and convolution kernels) now have a custom icon.
11 A command (SortPalette) that sorts the current look-up table by hue was added to the macro language.
12) PidNumber, a new macro function, was added to the macro language. It returns a negative permanent ID number for the current image. SelectPic and ChoosePic were modified to accept these negative values and find the current picNumber automatically if presented with a pid value rather than a picNumber value. A macro package (“PidNumbers Demo”) demonstrates the various ways that images can be selected in the macro language. The PidNumber modifications and demo macros were contributed by Edward J. Huff.
13) The line spacing in text windows is now changed when the font size is changed.
14) Text windows now handle update events correctly.
15) Plug-ins in the system folder in a folder named Plug-ins are now found if image is on a different volume than the the system folder.
16) The standard versions of NIH Image no longer requires a floating-point coprocessor (FPU). This change was made because there is no noticible performance difference between the FPU and non-FPU version of Image and becuase the LCIII and Centris 610, the most popular new Macs, do not have FPUs. This change also anticipates PowerPC based Macs which will not support emulation of 68000 programs that directly use the FPU.
