Catalog of Free Flow Cytometry Software | Purdue University Cytometry Laboratories

This catalog strives to be complete — to incorporate as a lot free stream cytometry software program as potential. We’ve got apart from added some demonstrations of business packages. Report feedback, catalogue omissions and corrections to jpr @ flowcyt.cyto.purdue.edu. Issues getting program information? right here ‘s HELP .

Purdue Free software program is all listed on one other web page – you’ll be able to go right here to seek out Cytospec, or PlateAnalyzer

Cytospec is beneficial for hyperspectral psychoanalysis and is a in reality simple program to make use of and does PCA american samoa nicely on common listmode information PlateAnalyzer handles a lot of massive knowledge units – any concern of parameters – can deal with CyTOF knowledge no issues, does excessive throughput screening utilizing 96, 384 nicely plates properly. Does dose response curves, and has a large number of advance options .

Walter & Eliza Corridor

free Software program is right here

 

Flowing Software program ( Perttu Terho )

Turku, Finland )

There’s apart from CYFLOGIC from right here however it has not been up to date for a very long time …Right here is the hyperlink 

 

Bioconductor

This can be a set of instruments based mostly on open code with “ R ” – it is advisable be a chew superior to make use of these instruments. right here is the hyperlink

Circulate Cytomery Instruments ( Jonathan Friedman andEugene Yurtsev)

A correctly bundle whcih you’ll be able to obtain from right here. FlowCytometryTools is a python bundle for visible picture and evaluation of high-throughput stream cytometry knowledge .

Multi-Function Evaluation Packages

Cell Cycle/DNA Evaluation

Cluster Evaluation

Different Particular Function

  • Kind Restoration Calculator (Runs on the internet!)
  • FACSLOG (HP 310/340, logs FACS use)
  • FACSOVL (PC/Home windows) Smooths, overlays Coulter XL histograms.
  • PeCAN (PC DOS) Gated quadrant/octant evaluation.
  •  

Knowledge Switch from Hewlett-Packard to PC/Mac

Miscellaneous PC Utilities

Miscellaneous Macintosh Utilities

  • FCS Assistant (Mac)
  • DropPrint (Mac, for CellQuest cytometer settings)
  • MacNormalize (Mac)

Home windows A number of Doc Interface

Greatest obtainable for normal functions ; coloured areas, quadrant evaluation, complicated gate. beautiful graphics, 3D contour and division of transportation plots. Created by Joseph Trotter of the Scripps Analysis Institute. WinMDI ( Win dows M ultiple D ocument I nterafce for Circulate Cytometry ) Requires MicroSoft Home windows 3.1 or higher. model 2.5 requires a 486 or higher processor. If it is advisable run underneath voiced Home windows on a Macintosh, get the particular model that makes use of the 286 educating set. A free-standing slideshow is obtainable which demonstrates WinMDI’s graphics. This slideshow operates underneath DOS (it doesn’t require Home windows). It’s obtainable as a self-unzipping file, WMDISHOW.EXE. Working the present could be very easy. Directions are included. Bounce again to contents. Again to software program index.

Median Fluorescence Depth

Quick batch evaluation of listmode information together with graphics and overlays, in full corrected intensities, automated peak detection, kinetics, calculated parameters, gate ratios. Spreadsheet-ready medians. Labels listmode information, converts to listmode or histogram knowledge to ASCII for spreadsheets. tutorial with pattern knowledge. ( Doesn’t do quadrant psychoanalysis. ) Works completely in Home windows.
Full documentation and the plan can be found from the MFI Residence web page Bounce again to contents. Again to software program index. That is the one free cluster evaluation software program obtainable for PC’s. Cytometry 14:649-659, 1993. Writer: Tom Bakker Schut, Netherlands. Richard Allen Cox is enhancing AUTOKLUS. For additional details about the standing of this undertaking, see the Circulate Cytometry Help Residence Web page. unique free Schut AUTOKLUS program.
details about the embody program
Included generator code
Included datum information Bounce binding to contents. Again to software program index. Normal objective platform with many graph codecs to facilitate the inclusion of multi-parameter knowledge. Contains : 1D histos, lineplot, persona show, dotplot, contours, floor diagram, 3D level plot, 3D iso-surface ; kinetic show of bastardly, +/- 1 std.dev., cv v clock time. apart from offers cell cycle evaluation, neural web bunch, batch temper help, composite graph technology ( from a number of information ), as much as 10 rectangular or irregular areas of curiosity for colour spotlight between parameters or modifying, and several other types of hardcopy output ( PS, HPGL, PCL, GIF, PICT ). IDLYK is a free script for a industrial interpreter “ IDL ”, which prices $ 1,500 per central processing unit ( private laptop or MAC ; extra for unix/VMS ). many universities have present IDL licenses on community servers ( ask from Jim Hill at Analysis Methods, Inc., the start of IDL, jimh @ rsinc.com ). examine from the author : Robb Habbersett, Los Alamos Nationwide Lab, NM USA ; robb @ beatrice.lanl.gov. Bounce again to contents. Again to software program index.

Laboratory Evaluation Program

Enter restricted to 1D and 2D histogram FCS knowledge solely ( doesn’t deal with listmode knowledge ). knock-down and compromising normal objective knowledge psychoanalysis and dealing with interpreter which makes use of FCS-type storage format. Does histogram overlays, 2D and 3D contour plots. Scripts exist for menstruation knowledge which might be reprogrammed as wanted. Request program from writer : John Powell, NIH, Bethesda MD USA, jip @ helix.nih.gov. Bounce again to contents. Again to software program index. Normal perform with polygonal gates ( mouse managed ), contour and density plots, histogram overlays, kinetics vs. occasion quantity and file slit. New parameters might be created by transformation and division. Helps just one printer, the HP Paintjet. Comp Biomed Res 27:83-96, 1994. writer : Tom Bakker Schut ( see underneath AUTOKLUS ) states that no foster exploitation is anticipated. column feedback : WinMDI is preferable for many functions, though ANALYSE has a number of singular options. ANALYSE is ten to 5 occasions slower than WinMDI or MFI to learn a listmode file. Due to its Home windows interface, WinMDI helps a a lot broad scope of printers. WinMDI has extra versatile gate logic, higher numeric outcomes for histograms and marked segments of histograms, higher management of colour or line sort for overlie histogram. -Eric Martz Bounce spinal column to contents. Again to software program exponent. Shows Coulter XL histogram information whereas smoothing, scaling, altering settlement ; overlays as much as 8 ; outputs to ASCII for spreadsheets. generator : Frederik Lindberg, Wash U, St Louis MO USA. lindberg @ visar.wustl.edu. Get self-unzipping program FXOVLZIP.EXE by file switch protocol. Bounce again to contents. Again to software program index.

PC ANalysis

That is an outdated however elegant disperse gate and quadrant evaluation program offered to the general public data area by Becton-Dickinson. It determines share optimistic cells from FCS1.0 information for one, two, or three colour work. It helps polygonal gates, requires EGA, and places out compendious information in ASCII database format ( e.g. appropriate for Lotus ). After you might have set the gate ( sometimes on FSC vs. SSC or scatter vs. FL3 = propidium iodide ), and set a division line for optimistic/adverse on every semblance ( it should routinely set the division for 99 % adverse in your management cells ! ), it processes all information within the present listing with out far therapy. nevertheless, it shows the acid plot and histograms for every file for a user-specified variety of seconds throughout which urgent any key permits modifications. simple-minded however truly fairly glib. Most VGA screens help the EGA it requires. PeCAN was written by Morgan Conrad and Ravi Mhatre whereas at B-D. C starting code is included. Get PeCAN from the CD-ROM.
Get PeCAN supply code from the CD-ROM. Bounce again to contents. Again to software program index. This verification suite offers instruments for producing FCS ( Circulate Cytometry Customary format ) knowledge information with know contents. It’s offered as a companion to MFI however is fascinating for verification of any platform ready of studying generic FCS information. Assessments with artificial knowledge symbolize one in all a number of strategies of verifying accuracy of outcomes. The included datum information can be utilized underneath any operational association, however the applications run lone underneath private laptop DOS ( or in a DOS window underneath MS Home windows ). nevertheless, the applications can be utilized underneath DOS to generate further knowledge information which might then be moved to any function group. The suite consists of this system A2FCS.EXE which converts ASCII spreadsheet-style knowledge information to FCS. It could possibly deal with 8- or 16-bit knowledge, and might mark the information as log-acquired. Applications are offered to generate column of random numbers ; the outcomes ( medians and many others. ) might be independently obtained by the circulation cytometry program of your alternative, and by generic spreadsheet software program for verification. The applications can generate randomly boastfully FCS information of repeating cycles of random numbers ( therefore with know medians, and so forth ). MFI has been examined utilizing this technique for as much as 2,000,000 occasions of three parameters every. ( Instruments are apart from offered for producing knowledge to show the greet of your alternative as a dot plat. ) Additional particulars can be found within the MFI/FCS Verification Suite documentation. MFI/FCS Verification Suite
Model 1.1 launched 8/16/96 corrects the $ BYTEORDer which was reversed ; due to Richard Carson. Bounce again to contents. Again to software program index. This program converts numeral knowledge in an ASCII file to an FCS file which might be learn by cling evaluation software program. The ASCII file might be created by a spreadsheet or every other means. Since MFI, WinMDI, and different software program can convert FCS information to ASCII information, one might edit the information in any approach desired after which re-convert to FCS. This utility program permits check knowledge generated mathematically for use to check circulation evaluation software program. generator : Joseph Trotter, Scripps Analysis Institute, La Jolla CA. trotter @ scripps.edu. discover : an alternate execution, A2FCS.EXE, is obtainable within the MFI/FCS Verification Suite. Get the Text2FCS program from the CD-ROM or by file switch protocol from the Scripps Institute. Bounce again to contents. Again to software program index. FACSLOG is suite of 4 applications to handle consumer entree of HP 9000/310 and 9000/340 laptop methods. It might be began mechanically or manually after the pc has booted. Customers can be required to “ log in ” with their initials and a password. An optionally available “ welcome ” or “ information ” display screen is displayed at login. log in and log-out dates and occasions for every drug consumer are recorded in a knowledge file, which can be searched and printed by date and the customers ‘ “ group ” task ( reminiscent of lab affiliation or placard historical past quantity ). This knowledge could apart from be saved in a file fascinating for consequence in spreadsheet or database applications. fully “ System Directors ” could enter and take away customers or make adjustments to the system-use log file. FACSLOG was created by Neal A. Benson, College of Florida, Gainesville FL USA, nbenson @ nervm.nerdc.ufl.edu. Get FACSLOG from the CD-ROM. Bounce again to contents. Again to software program index. Hewlett-Packard ( HP ) computer systems offered with FACS devices have been a lot bundled with Hewlett-Packard Paintjet colour printers. These printers sometimes have solely an IEEE-488 GPIB connection ( fairly than the usual Centronics parallel printer connection anticipated by a private laptop ). nevertheless, you probably have an IEEE-488 GPIB card in your private laptop ( see HPPCLINK ), you can’t lone transer information between the HP and PC, however you’ll be able to print instantly from the private laptop to the Paintjet. right here you may get an ASCII textual content file, PAINT488.TXT, containing element directions on how to do that. Bounce wager on to contents. Again to software program index. The Purdue Utilities are a household of applications which embody the next : GENP takes a two argument correlated FCS histogram, and generates a listing of ‘factors ‘ and ‘weights ‘ from it. It’s designed to generate a listing of scatterplot factors to be learn by some early evaluation, statistics, or graphics broadcast.
GENP software program documentation. KEYS is used to generate numerous all of the keyword-value pair in an FCS file. This consists of the FCS TEXT and ANALYSIS segments, however not any non-public segments. [ MFI displays text block keyword-value pairs to the screen from a point-and-shoot menu of filenames ; it does not display the analysis stop. ]
KEYS documentation. LDATA reads an FCS histogram file and writes its uncooked datum section to the display screen or to an ASCII file. It’s used when it’s commodious to have histogram knowledge in a human clear format, or when the information must be learn by a criterion evaluation or statistics program. [ MFI can write a gate, smoothed ASCII histogram data file from the list mode file. ]
LDATA software program documentation. LLDATA is used to generate a textbook itemizing of the information in a listmode file. [ MFI can produce a gate ASCII charge of list mode data from an FCS list modality file. ]
LLDATA software program documentation.

LOOKUP opens FCS information, and retrieves particular key phrase values.
LOOKUP software program documentation. SETKEY is used to alter the speed of a key phrase in an FCS file or so as to add newly key phrases to the file. [ MFI can change values of keywords which are not critical to data integrity, or add new keywords and values. ]
SETKEY software program documentation. Authors : J. Paul Robinson and Steve Kelley, Purdue Univ., West Lafayette IN USA. kelley @ flowcyt.cyto.purdue.edu. Bounce rear to contents. Again to software program index.

(John Curtin Faculty)

This syndicate of utilities consists of FCSVIEW, a elementary program to plot histograms out particularly on a HP pen conspirator ( in HPGL ). One other utility program reverses the byte order of the binary listmode knowledge in FCS1.0 information. examine from Geoffrey Osborne, John Curtin Faculty of Medical Analysis, Australian Nationwide College, Canberra geoff.osborne @ anu.edu.au. Bounce again to contents. Again to software program index. A waterproof coat utility to transform FCS1.0 and a couple of.0 information to textual content. It apart from provides rely ratio, and time parameters and saves in FCS2.0. The course of examine outputs three sorts of textual content file : uncooked listing mode knowledge, histogram knowledge, and line graph knowledge ( eg imply Calcium 5 Time ). It could possibly deal with as much as 16 parameters, and permits the exploiter to delete pleonastic parameters to create space. B-D vax, HP, and Mac information are opened as are Coulter IBM information. At painting solely Mac format FCS2.0 information are exported, however in future variations this system will save in FCS1.0 codecs ( LYSYS, consort 30, FACScan and many others ) to permit customers of older methods entry to ratio and meter. ( Editor ‘s notice : MFI, a DOS bundle, apart from calculates and normalizes the proportion of two present parameters, and plots any argument vs. time or pseudo-time [ event number ]. It could possibly put the outcomes out into ASCII listmode or histogram information. Its firm course of examine A2FCS can convert the ASCII listmode with account parameter into an FCS2.0 file. See apart from Refresh Ratio. ) Compiler/Language : Written in Suppose Pascal 4.0.2 for the Macintosh utilizing ThinkClass Library version1.1. Supply Code : “ apart from embarrass to Distribute ”. generator : Ray Hicks rh208 @ cus.cam.ac.uk Get FCS Assistant from the CD-ROM. Bounce binding to contents. Again to software program index. Prints cytometer settings as recorded in information acquired with CellQuest ( thulium Becton-Dickinson ) model 1.1 or larger, from FACScan, FACSort, or FACSCalibur devices. Offered with out assure by its generator, Ted Kunich, TedKunich @ worth.web. Get DropPrint from the CD-ROM. invoice : You have to a model of Stuff-it Expander to unpack this program. Bounce again to contents. Again to software program index. Normalizes circulation cytometric immunophenotyping knowledge to a organic customary. This program is underneath improvement. Contact Gary Salzman, Los Alamos Nationwide Laboratory, Los Alamos NM USA. salzman @ lanl.gov. Bounce again to contents. Again to software program index. This PC/Home windows program refreshes the present ratio of two user-specified parameters in LYSYS II listmode information ( B-D FACScan, FACStar ), or creates a brand new ratio argument. It’s untested on different FCS2.0 information. suitable with linear or log knowledge, 256 or 1024 duct resolving energy. In some devices, the {hardware}/software program will not be flying sufficient to generate a proper proportion worth for all occasions ; Refresh Ratio fixes this downside. The generator is Ron Hoebe on the College of Amsterdam, Netherlands, r.hoebe @ amc.uva.nl. Report issues or incompatibilities to him. ( This system was written in Visible Primary 3.0 for Home windows. Supply code will not be offered. ) Catalog editor program ‘s notice : MFI ( see elsewhere on this catalogue ) can calculate the ratio of two user-specified parameters, and rescale the consequence in a number of optionally available methods. Not like Refresh Ratio, MFI calculates the proportion throughout psychoanalysis, and doesn’t write it to the listmode file. Get Refresh Ratio, or go to their house web page. Bounce spinal column to contents. Again to software program index. Self extracting archive. HPDIR.EXE and HPCOPY.EXE use BIOS calls to learn from a PC 3.5″ drive HP LIF floppies formatted utilizing possibility 16 of MEDIAINIT. HPDIR shows the listing of an HP floppy, and HPCOPY copies one or all information from the HP floppy to a DOS listing. Applications are courtesy of Pier-Luigi Lollini, Instituto di Cancerologia, Universita’ di Bologna. get Applications from CD-ROM
To unpack, plainly copy this system to an empty listing and execute it. Bounce again to contents. Again to software program index. This can be a pair of applications which switch information, together with listmode information, between Hewlett-Packard ( HP ) Pascal 3.1 computer systems and private laptop ‘s. switch can happen in both course. Therefore, PC copies of information can function backing which might be transferred spinal column to the HP for psychoanalysis with HP software program. private laptop copies of listmode information can apart from be used with evaluation software program reminiscent of WinMDI and MFI. switch takes about 30 seconds per 10,000 occasion listmode file. Different switch software program offered by Verity, which makes use of the identical {hardware}, is alleged to switch information nicely sooner. ( Verity Software program Home, Inc., Topsham ME USA. 207-729-6767. reality @ vsh.com ) use of those applications requires an IEEE-488 GPIB wag for the private laptop. such playing cards value about $ 500. One vendor which offers glorious technical help is Nationwide Devices, gpib_support @ natinst.com, accessible on the Nationwide Devices internet website online. One other answer is the OptiMATE field ( board plus quick industrial software program ) from Utilized Cytometry Methods. The private laptop program HPPCLINK.EXE is included within the self-unzipping file HP2PC.EXE. The HP broadcast HPPCLINK.CODE can apart from be gotten right here bundled with instruments which allow you to place it on an HP-formatted diskette. The directions, in HPPCLINK.TXT, are included within the bundle platform, X2FF10LK.EXE. Due to Scott Rouse for determining how to do that ! ( This methodology will permit any public sphere HP program to be transferred through Web. ) For much steerage on 4 potential methods to switch information between HP ‘s and PC ‘s, see the file HP2PC.TXT. These applications have been offered to the general public world by Becton-Dickinson. Bounce again to contents. Again to software program exponent. This can be a pair of applications which switch information, together with listmode information, between Hewlett-Packard ( HP ) Pascal 3.1 computer systems and private laptop ‘s through a serial port cable. Switch is carried out solely within the HP to PC course. private laptop copies of listmode information can be utilized with psychoanalysis software program reminiscent of WinMDI and MFI. Switch takes a number of minutes per listmode file. frankincense, transferring a bunch of information can take respective hours. To make issues worse, the HPTOIBM program comprises a tease which makes it transmit solely each second file. After it has been run, if the primary file within the sequence is moved elsewhere, and this system restarted, it should switch the interchange information it skipped through the starting streak. thus, the course of examine should be run twice for each group of information to be transferred. This tease was fastened, however the fastened model of this system has not been situated in holocene years. Particularly, inquiries with Becton-Dickinson, and with the writer, Morgan Conrad, have been bootless. The private laptop program FROMHP.COM is included within the self-unzipping file HP2PC.EXE. The HP program HPTOIBM.CODE should usually be obtained by snail mail on an HP-format diskette. It’s because most HP Pascal 3.1 computer systems do not need an ethernet port, so the diskette drive is the lone approach to get an exterior file into the pc. Ethernet ports for these computer systems are so costly as to be prohibitive for many amenities. To place it one other method, in case your HP had an ethernet port, you’ll n’t want HPTOIBM.CODE ! To acquire the HP course of examine, contact emartz @ microbio.umass.edu. For additional steering on 4 potential methods to switch information between HP ‘s and PC ‘s, see the file HP2PC.TXT. These applications have been offered to the general public area by Becton-Dickinson. Bounce again to contents. Again to software program index.

Resonance Vitality Switch Depth

Calculates RETI, e.g. for donor = fluorescein, acceptor = tetramethyl rhodamine. Requires enter sign of 12 values ( 4 autofluorescence, 8 donor-excited [ e.g. 488 nanometer ; 4 detected park, 4 bolshevik ], 4 acceptor-excited [ e.g. 514 nanometer ] ) to calculate one RETI respect. Math checked by Janos Szollosi. Enter batched through ASCII file. MFI ( see above ) was designed to generate the 12 enter sign medians effectively. author : Eric Martz, Univ. Mass., Amherst MA USA. emartz @ microbio.umass.edu. If , request by e mail to have the newest model put up on the ftp server. Get RETI by from the CD-ROM. Bounce again to contents. Again to software program index.

Corrected Fluorescence Depth

Accepts log-acquired median or beggarly intensities typed manually. Converts log values to a linear quantity scale, optionally subtracting management worth and/or rescaling to MESF. C supply code included. generator : Eric Martz, Univ. Mass., Amherst MA USA. emartz @ microbio.umass.edu. Get CFI program from the CD-ROM.
CFI Readme file and License. Bounce again to contents. Again to software program index. This can be a JavaScript program written by Joseph Trotter on the Scripps Institute, which calculates estimated restoration statistics for sorting.
Run the script. Bounce spinal column to contents. Again to software program index. All of the DOS applications on this assortment are within the type of ZIP archives or self-extracting EXE information.
There’s a absolve translation of UNZIP.EXE right here. Macintosh applications all through the harrow are within the form of BinHex encoded Stuffit Expander archives. Some Mac applications are self-extracting ( after being un-BinHexed ), whereas others should be explicitly extracted by a StuffitExpander suitable prlgram. Stuffit Expander is obtainable right here, however it’s in BinHex format apart from, and you have to purchase a plan able to decoding BinHex paperwork elsewhere. The browsers used to navigate this 4 hundred ought to supply the choice of downloading these information to your laborious disk when the hyperlinks are clicked on. As well as, you’ll be able to copy the information instantly from the compact disk to your laborious disk. Every of those applications is in its personal listing within the 3data listing of the cadmium. Multiplex Software program See Purdue Cytometry Labs for Mutliplex software program TASBE Circulate Analytics – Jake Beal TASBE is a calibrate menstruate cytometry bundle based mostly on Matlab/Octave and aimed toward unit calibration and quantitative evaluation. It was developed it within the context of various artificial biology analysis tasks, and it ‘s been utilized in knowledge evaluation for numerous publications.

Bounce again to contents. Again to software program index .

Related Posts

Leave a Reply

Your email address will not be published.