SOMBatch Ver IV (c) Stephen H. Cody These are a list of macro commands that run under MPL or SOM in Bio-Rad MRC-500, 600 or 1000 series confocal microscopes. You are welcome to use these batch files free to aid your research. Please do not distribute these macros. If used in collection and analysis of data please cite in the methods or acknowledgments: SOMBatch Ver. IV by Stephen H. Cody, Ludwig Institute for Cancer Research, Melbourne, Australia. 4d.cmd This command is for creating a 4D data set. It creates a TIME SERIES of Z-SERIES. It also saves the PROJECTION of each Z-SERIES. (C) Stephen H. Cody Stephen.Cody@ludwig.edu.au 7-05-2001 Align.cmd This command is to assist the user in realigning a specimen on the microscope stage, to its original position relative to a reference image. (c) Stephen Cody 1996 Stephen.Cody@ludwig.edu.au Biomedical Confocal Microscopy Research Centre Department of Pharmacology University of Western Australia Align1.cmd This command is to assist the user in realigning a specimen on the microscope stage, to its original position. It is recommended that F4 fast scan be set in CoMOS prior to using this command. Or use OVERLAY RESET from the MPL prompt (c) Stephen Cody 1996 Stephen.Cody@ludwig.edu.au Biomedical Confocal Microscopy Research Centre Department of Pharmacology University of Western Australia align2.cmd This command is to assist the user in realigning a specimen on the microscope stage, to its original position. It is recommended that F4 fast scan be set in CoMOS prior to using this command. The Yellow overlay will remain on the screen even after returning to CoMOS. To remove overlays run ALIGN.cmd again then QUIT (c) Stephen Cody 1996 Stephen.Cody@ludwig.edu.au Biomedical Confocal Microscopy Research Centre Department of Pharmacology University of Western Australia Autopack.cmd This command copies several different images into a single new file, as frames. The file names of the original images must consist of a common part followed by a number. This command may not work with some versions of Bio-Rad sofware. If you have difficulties use the PACK.CMD command instead. (c) Stephen Cody 1994 Stephen.Cody@ludwig.edu.au Bkdiv.cmd This command subtracts an image of the background, prior to making a ratio image of a dual channel (ie. side-by-side) image. BKDIV requires an image of the background, called BKGRD.PIC If your background image has a different name use NAMEDIV.CMD This command will work with z-series (or time-series) images. To quit enter Ctrl U (c) Stephen Cody 1994 Stephen.Cody@ludwig.edu.au Count.cmd This command facilitates cell counting by leaving a square on the cells already counted. To count cells use the RIGHT mouse button. (c) Stephen Cody 1994 Stephen.Cody@ludwig.edu.au Count2.cmd This command facilitates cell counting by leaving a square on the cells already counted. To count cells use the RIGHT mouse button. (c) Stephen Cody 1994 Stephen.Cody@ludwig.edu.au Dat.cmd Warning, This command only seems to run under MPL, Bummer! This command allows the STATS command to be executed on the same region of all images of a z-series . The results of the stats command, the MEAN and AREA of the GREEN band, are exported to a file called [File name].dat See also STATDAT.cmd, STATDAT2.cmd, ZSTATS2.cmd and ZSTATS.cmd (c) Stephen Cody 1994 Stephen.Cody@ludwig.edu.au Edit.cmd This command file will allow you to extract a common region from all sections of a zseries. And also allow rotations of this region. (c) Stephen Cody 1994 Stephen.Cody@ludwig.edu.au Findiv.cmd This command is for dividing one image file by another file. This command allows you to subtract a numerical value, representing the intensity of the background for each individual image, prior to making the ratio image. This command will work with z-series (or time-series) images. (c) Stephen Cody 1994 Stephen.Cody@ludwig.edu.au Flash.cmd This command is for conducting caged comound experiments. There are some software and hardware requirements before this command will work. You'll need an MRC-1000 UV system, with method buttons already set up. This command has to re-centre any PAN settings. (c) Stephen Cody and David WIlliams 1995 Stephen.Cody@ludwig.edu.au Fmandiv.cmd This command is for dividing one image file by another file. This command allows you to subtract a numerical value, representing the intensity of the background, prior to making the ratio image. This command will work with z-series (or time-series) images. (c) Stephen Cody 1994 Stephen.Cody@ludwig.edu.au Fnamediv.cmd This command is for dividing one image file by another file. Before the division process, background images will be subtracted. The command will prompt you for the name of these background images. This command will work with z-series (or time-series) images. (c) Stephen Cody 1994 Stephen.Cody@ludwig.edu.au Fredscn1.cmd WARNING, This command only works on the MRC-1000, utilizing MPL This command repetively collects ONE second, line scans pairs for dual excitation, (c) Stephen Cody 1994 Stephen.Cody@ludwig.edu.au Fredscn2.cmd WARNING, This command only works on the MRC-1000, utilizing MPL This command repetively collects TWO second, line scans pairs for dual excitation experiments. (c) Stephen Cody 1994 Stephen.Cody@ludwig.edu.au Fredscn6.cmd WARNING, This command only works on the MRC-1000, utilizing MPL This command repetively collects SIX second line scans pairs for dual excitation, (c) Stephen Cody 1994 Stephen.Cody@ludwig.edu.au Graph.cmd This macro will run the AREA command then leave the histogram overlay on the image. Use the OVERLAY command to make it permannant. (c) Stephen Cody 5-9-97 Stephen.Cody@ludwig.edu.au Make2x2.cmd This command is ONLY used by those with a CODONICS NP-1600 er and PCTCP networking software. This command facilitates creation of a 2 x 2 montage by giving a preview of what the final montage layout will be. A temporay DOS batch file called PRN2x2.bat will be created. PRN2x2 should then be run to the final montage The PRN2x2 batch file requires the SEND2X2.bat file in order to . (c) Stephen Cody 1996 Stephen.Cody@ludwig.edu.au Make2x3.cmd This command is ONLY used by those with a CODONICS NP-1600 er and PCTCP networking software. This command facilitates creation of a 2x3 montage by giving a preview of what the final montage layout will be. A temporay DOS batch file called PRNtmp.bat will be created. PRNtmp should then be run to the final montage. The PRNtmp batch file requires the SEND2x3.bat file in order to . (c) Stephen Cody 1996 Stephen.Cody@ludwig.edu.au MakeA4.cmd This command is ONLY used by those with a CODONICS NP-1600 er and PCTCP networking software. This command facilitates creation of an A4 single image . A temporay DOS batch file called PRNtmp.bat will be created. PRNtmp should then be run to the final A4 . The PRNtmp batch file requires the SENDA4.bat file in order to . (c) Stephen Cody 1996 Stephen.Cody@ludwig.edu.au Maketest.cmd This command is ONLY used by those with a CODONICS NP-1600 er and PCTCP networking software. This command creation a SERIES of TEST images at different er settings. This command is only used for setting up the er, and should only be used by microscopy STAFF ONLY"" A temporay DOS batch file called PRNtmp.bat will be created. PRNtmp should then be run to the final TEST . The PRNtmp batch file requires the SendTest.bat file in order to . (c) Stephen Cody 1996 Stephen.Cody@ludwig.edu.au Mandiv.cmd This command allows you to subtract a numerical value, representing the intensity of the background, prior to making a ratio image of a dual channel (ie. side-by-side) image. This command will work with z-series (or time-series) images. (c) Stephen Cody 1994 Stephen.Cody@ludwig.edu.au Mergefix.cmd This command allows the ALIGNment of an merged image and then performs a CONTRAST FIX routine on each image plane. You will be prompted for the MINIMUM and MAXIMUM values for the RED plane. The aligned and fixed images will then be saved as a 24 bit RGB image. (c) Stephen Cody 8-1-97 Stephen.Cody@ludwig.edu.au Mont.cmd This command is for creating montages using the motorised XY-Stage. It is assumed the stage is properly calibrated. To change direction of the XY-Stage movement, edit lines 8 & 9 of this file. Lines 8 & 9 will change the direction of stage movement. eg. Change "-" to "+" (c) Stephen Cody 1997 Stephen.Cody@ludwig.edu.au Mont2.cmd This command is for creating montages using the motorised XY-Stage. And is designed for DUAL LABELLING EXPERIMENTS. This command MUST be used with a MRC-1000 ONLY. It is assumed the stage is properly calibrated. To change direction of the XY-Stage movement, edit lines 8 & 9 of this file. Lines 8 & 9 will change the direction of stage movement. eg. Change "-" to "+" (c) Stephen Cody 1997 Stephen.Cody@ludwig.edu.au Montage.cmd This command is for creating montages using the motorised XY-Stage. It is assumed the stage is properly calibrated. To change direction of the XY-Stage movement, edit lines 8 & 9 of this file. Lines 8 & 9 will change the direction of stage movement. eg. Change "-" to "+" (c) Stephen Cody 1997 Stephen.Cody@ludwig.edu.au Movie.cmd This command rapidly displays the images in a z-series or time-series sequentially, and allows the MOVIE to repeat several times. This may not work on some versions of SOM. (c) Stephen Cody 1994 Stephen.Cody@ludwig.edu.au Namediv.cmd This command subtracts an image of the background, prior to making a ratio image of a dual channel (ie. side-by-side) image. This command will work with z-series (or time-series) images. (c) Stephen Cody 1994 Stephen.Cody@ludwig.edu.au Pack.cmd This command copies several different images into a single new file, as frames. Also see the AUTOPACK command (c) Stephen H. Cody 1994 Stephen.Cody@ludwig.edu.au Picname.cmd Still In Development (c) Stephen H. Cody 1994 Stephen.Cody@ludwig.edu.au Prigdat.cmd Warning, This command only seems to run under MPL, Bummer! This command allows the STATS command to be executed on the same region of all images of a z-series . The results of the stats command, the MEAN and AREA of the GREEN band, are exported to a file called [File name].dat See also STATDAT.cmd, STATDAT2.cmd, ZSTATS2.cmd and ZSTATS.cmd (c) Stephen H. Cody 1994, 1996 Stephen.Cody@ludwig.edu.au Scan1.cmd This command repeats a ONE second line scan, with a pause between scans. (c) Stephen H. Cody 1994 Stephen.Cody@ludwig.edu.au Scan2.cmd This command repeats a TWO second line scan, with a pause between scans. (c) Stephen H. Cody 1994 Stephen.Cody@ludwig.edu.au Scan6.cmd This command repeats a SIX second line scan, with a pause between scans. (c) Stephen H. Cody 1994 Stephen.Cody@ludwig.edu.au Stack.cmd This command copies several different z-series images, into a new z-series file. (c) Stephen H. Cody 1994 Stephen.Cody@ludwig.edu.au Statdat.cmd Warning, This command only seems to run under MPL, Bummer! This command allows the STATS command to be executed on the same region of all images of a z-series . The results of the stats command, the mean and means of all bands, are exported to a file called STATDAT.dat See also STATDAT2.cmd, ZSTATS2.cmd and ZSTATS.cmd (c) Stephen H. Cody 1994 Stephen.Cody@ludwig.edu.au Statdat2.cmd Warning, This command only seems to run under MPL, Bummer! This command allows the STATS command to be executed on the same region of both channels of a two channel image . Then repeated in all images if the file is a z-series . The results of the stats command, the mean and means of all bands, are exported to files called LEFT.dat and RIGHT.dat See also STATDAT.cmd, ZSTATS2.cmd and ZSTATS.cmd (c) Stephen H. Cody 1994 Stephen.Cody@ludwig.edu.au Statdatm.cmd Warning, This command only seems to run under MPL, Bummer! This command allows the STATS command to be executed on the same region of all images of a z-series . The results of the stats command, the mean and means of all bands, are exported to a file called STATDAT.dat See also STATDAT2.cmd, ZSTATS2.cmd and ZSTATS.cmd (c) Stephen H. Cody 1994 Stephen.Cody@ludwig.edu.au Statdats.cmd Warning, This command only seems to run under MPL, Bummer! This command allows the STATS command to be executed on the same region of both IMAGES of a SEQUENCE. Then repeated in all images if the file is a z-series . The results of the stats command, the mean and means of all bands, are exported to files called .dat and .dat See also STATDAT.cmd, ZSTATS2.cmd and ZSTATS.cmd (c) Stephen H. Cody 1994 Stephen.Cody@ludwig.edu.au Strip.cmd This command file will allow you to extract a common region from all sections of a zseries. And also allow rotations of this region. (c) Stephen H. Cody 1994 Stephen.Cody@ludwig.edu.au Strip2.cmd This command will allow you to extract matching common regions from both channels of a two channel image and all sections of a zseries. And also allow rotations of this region. (c) Stephen H. Cody 1994 Stephen.Cody@ludwig.edu.au Thumb.cmd This command creates THUMBNAIL images with just the file name displayed on each image. The images that have already been displayed in a thumbnail are MARKED, so you don't get the same image twice. If you make a mistake typing in the file names THUMB will abort. Sorry but there is not much I can do about that. After an abort you can CONTINUE your THUMBNAIL by using the "THUMoops" command. (c) Stephen H. Cody 1996 Stephen.Cody@ludwig.edu.au Thumb2.cmd This command creates THUMBNAIL images with just the file name displayed on each image. If the image to be displayed is a Z-SERIES the MAXIMUM intensity PROJECTION is displayed. The images that have already been displayed in a thumbnail are MARKED, so you don't get the same image twice. If you make a mistake typing in the file names THUMB will abort. Sorry but there is not much I can do about that. After an abort you can CONTINUE your THUMBNAIL by using the "THUMoops" command. (c) Stephen H. Cody 1996 Stephen.Cody@ludwig.edu.au Thumoop2.cmd This command continues a THUMBNAIL after an abort from the THUMB command Don't use this command on its own. It should only be used after THUMB.cmd (c) Stephen H. Cody 1996 Stephen.Cody@ludwig.edu.au Thumoops.cmd This command continues a THUMBNAIL after an abort from the THUMB command Don't use this command on its own. It should only be used after THUMB.cmd (c) Stephen H. Cody 1996 Stephen.Cody@ludwig.edu.au Thump.cmd This command creates THUMBNAIL images with just the file name displayed on each image. If one or more images are Z-SERIES the MAXIMUM intensity PROJECTION of these files is displayed. This command is most useful if you have some Z-series files. For TIME-SERIES see the related commands THUMT.cmd and THUMPT.cmd The images that have already been displayed in a thumbnail are MARKED, so you don't get the same image twice. If you make a mistake typing in the file names THUMB will abort. Sorry but there is not much I can do about that. After an abort you can CONTINUE your THUMBNAIL by using the "THUMoops" command. (c) Stephen H. Cody 1996 Stephen.Cody@ludwig.edu.au Thumpt.cmd This command creates THUMBNAIL images with just the file name displayed on each image. If the image to be displayed is a Z-SERIES you have the choice of displaying the MAXIMUM intensity PROJECTION or one image from the series. This command is most useful if you have a mixture of Z-series and T-series Also see related commands THUMP.cmd and THUMT.cmd The images that have already been displayed in a thumbnail are MARKED, so you don't get the same image twice. If you make a mistake typing in the file names THUMB will abort. Sorry but there is not much I can do about that. After an abort you can CONTINUE your THUMBNAIL by using the "THUMoops" command. (c) Stephen H. Cody 1996 Stephen.Cody@ludwig.edu.au Unpack.cmd This command copies the frames of an image to seperate images. (c) Stephen H. Cody 1994 Stephen.Cody@ludwig.edu.au Vesdat.cmd Warning, This command only seems to run under MPL, Bummer! This command allows the STATS command to be executed on the same region of all images of a z-series . The results of the stats command, total intensity, and pixel no., for the red band, are exported to a file called "<"filename">".dat Custom prepared for Alan Everett, Physiology, UWA. For Motor End Plate Vesicle Measurements (c) Stephen H. Cody 1996 Stephen.Cody@ludwig.edu.au Biomedical Confocal Medical Research Centre Department of Pharmacology University of Western Australia Vesdat2.cmd Warning, This command only seems to run under MPL, Bummer! This command allows the STATS command to be executed on the same region of all images of a z-series . The results of total intensity, and pixel no. are calculated Custom prepared for Alan Everett, Physiology, UWA. For Motor End Plate Vesicle Measurements (c) Stephen H. Cody 1996 Stephen.Cody@ludwig.edu.au Biomedical Confocal Medical Research Centre Department of Pharmacology University of Western Australia Zbase.cmd This command subtracts a numerical value form a zseries of images (c) Stephen H. Cody 1994 Stephen.Cody@ludwig.edu.au Zbase2.cmd This command subtracts numerical values from both channels of two channel zseries of images (c) Stephen H. Cody 1994 Stephen.Cody@ludwig.edu.au Zbasetmp.cmd Still being developed This command subtracts a numerical value form a zseries of images (c) Stephen H. Cody 1994 Stephen.Cody@ludwig.edu.au Zclear.cmd This command erases a common region from all files in a series, then saves altered images to a new file. If * is specified (ie. @zclear *) then the command may overwrite an existing file without a warning. BE CAREFUL. This may be useful if you wish to overwrite the input file ie. the input file is the same as the output file. (c) Stephen H. Cody 1994 Stephen.Cody@ludwig.edu.au Zcont.cmd This command adjusts the contrast of a Z-series of images and saves the altered image into a new file. (c) Stephen H. Cody 1996 Stephen.Cody@ludwig.edu.au Zcont2.cmd This command adjusts the contrast of a Z-series of images and saves the altered image into a new file. (c) Stephen H. Cody 1996 Stephen.Cody@ludwig.edu.au Zfactor.cmd This command calculates the Z-Factor required in 3D reconstructions so that VOXELS are isotropic "("ie. cubic")". There seems to be a problem with CoMOS not reporting the correct Z-STEP in the image header, check the green overlay notes while stepping through the images before continuing. (c) Stephen H. Cody 4 April 1997 Stephen.Cody@ludwig.edu.au Zflip.cmd This command copies a Z-series of images into a new file in reverse order. See also ZEDIT, UNPACK, AUTOPACK and PACK commands This command may not work with some versions of Bio-Rad sofware. If you have difficulties use the PACK.CMD or UNPACK commands instead. (c) Stephen H. Cody 1996 Stephen.Cody@ludwig.edu.au Zgamma.cmd GAMMA value Copyright 1993 by Bio-Rad Microscience Create greyscale gamma lookup tables : 1 gives default This command alters the GAMMA value of all images in a z-series. Modified by Stephen Cody Nov. 12 1996 Stephen.Cody@ludwig.edu.au Zlen.cmd This command allows the LENGTH command to executed along the same line of all images in a z-series > Use the same parameters as for the LENGTH internal command (c) Stephen H. Cody 1994 Stephen.Cody@ludwig.edu.au Zlendat.cmd This command allows the LENGTH command to executed along the same line of all images in a z-series Use the same parameters as for the LENGTH internal command Type "HELP LENGTH" at the command prompt for details. The LENGTH statistics are written to a data file. (c) Stephen H. Cody 1994 Stephen.Cody@ludwig.edu.au Zlenprig.cmd This command allows the LENGTH command to executed along the same line of all images in a z-series Use the same parameters as for the LENGTH internal command Type "HELP LENGTH" at the command prompt for details. The LENGTH statistics are written to a data file. (c) Stephen H. Cody 1994, 1996 Stephen.Cody@ludwig.edu.au Zmed.cmd This command applies a MEDIAN filter to all images in a z-series (c) Stephen H. Cody 1996 Stephen.Cody@ludwig.edu.au Zmont.cmd This command is for creating a montage of z-projections, and saving a SAMPLE of the z-series at a variable number of sites. It is assumed the stage is properly calibrated. To change direction of the XY-Stage movement, edit lines 8 & 9 of this file. Lines 8 & 9 will change the direction of stage movement. eg. Change "-" to "+" (c) Stephen H. Cody 12-9-97 Stephen.Cody@ludwig.edu.au Zpaste.cmd This command file will allow you to MOVE &/or ROTATE a common region from all sections of a zseries. And treat any matched images from a SEQUENCE of images in the same manner (c) Stephen H. Cody 1996 Stephen.Cody@ludwig.edu.au It is recommended that you use the STRIP.cmd afterwards. Zpastesq.cmd This command file will allow you to MOVE &/or ROTATE a common region from all sections of a zseries. And treat matched images from a SEQUENCE of images in the same manner (c) Stephen H. Cody 1996 Stephen.Cody@ludwig.edu.au It is recommended that you use STRIP.cmd afterwards Zsplit.cmd This command will separate a two channel image into two files, and repeat the process for all the images in the z-series. (c) Stephen H. Cody 1-6-97 Stephen.Cody@ludwig.edu.au Zsatat.cmd Warning, This command only seems to run under MPL, Bummer! This command allows the STATS command to be executed on the same region of all images of a z-series . The results of the stats command, the MEAN and AREA of the GREEN band, are exported to a file called [File name].dat See also STATDAT.cmd, STATDAT2.cmd, ZSTATS2.cmd and ZSTATS.cmd (c) Stephen H. Cody 27-5-97 Stephen.Cody@ludwig.edu.au Zstat2.cmd Warning, This command only seems to run under MPL, Bummer! This command allows the STATS command to be executed on the same region of both channels of a two channel image . Then repeated in all images if the file is a z-series . The results of the stats command are exported to a DATA file See also STATDAT.cmd, ZSTATS2.cmd and ZSTATS.cmd (c) Stephen H. Cody 27-5-97 Stephen.Cody@ludwig.edu.au Zstat2m.cmd Warning, This command only seems to run under MPL, Bummer! This command allows the STATS command to be executed on the same region of both channels of a two channel image . Then repeated in all images if the file is a z-series . The results of the stats command are exported to a DATA file See also STATDAT.cmd, ZSTATS2.cmd and ZSTATS.cmd (c) Stephen H. Cody 27-5-97 Stephen.Cody@ludwig.edu.au Zstats.cmd This command allows the STATS command to executed on the same region of all images in a z-series . See also ZSTATS2.cmd Use ZSTATS * to skip histogram plot. (c) Stephen H. Cody 1994 Stephen.Cody@ludwig.edu.au Zstats2 This command allows the STATS command to executed on the same region of both channels of a two channel image . Then repeated in all images if file is a z-series . See also ZSTATS.cmd Use ZSTATS2 * to skip histogram plot. (c) Stephen H. Cody 1994 Stephen.Cody@ludwig.edu.au Zstat2m.cmd This command allows the STATS command to executed on the same region of both channels of a two channel image . A new region is then drawn for the remaining images in the z-series. See also ZSTATS2.cmd and ZSTATS.cmd (c) Stephen H. Cody 1994 Stephen.Cody@ludwig.edu.au Zstatsm.cmd This command allows the STATS command to executed on the same region of both channels of a two channel image . A new region is then drawn for the remaining images in the z-series. See also ZSTATS2.cmd and ZSTATS.cmd (c) Stephen H. Cody 1994 Stephen.Cody@ludwig.edu.au Zstrip.cmd This command file will allow you to extract a common region from all sections of a zseries. And also allow rotations of this region. (c) Stephen H. Cody 1994 Stephen.Cody@ludwig.edu.au Ztseries.cmd This command is for creating a TIME SERIES of Z-PROJECTIONS . (c) Stephen H. Cody 1996 Stephen.Cody@ludwig.edu.au Zxtract.cmd This command file will allow you to extract a common region from all sections of a zseries. And also allow rotations of this region. (c) Stephen Cody 1994 Stephen.Cody@ludwig.edu.au