STEM_CELL

Index

  • Terms of use
  • A short story of this idea
  • Before download
  • —-> Download  <——-
  • Installation instruction
  • Manual
  • Related articles
  • FAQ

Terms of use

The software stemcell is freely available and part of its sources can be also requested by email …
I only ask you to cite my articles containing a reference to the specific function you are using or (for the moment) this web site. Alas in this situation only a limited support will be given apart form the manual. Bug reporting is always welcome anyway.
Conversely if you feel you need more advanced functions, support, training or scientific experise feel free to contact me for a collaboration. In particular feel free to cantact me for simulation of the HAADF contrast.
Since the STEM_CELL process is still under developement a limited part of the function is available in the free version but more will be added the next months. For a list of the main fetures already available go to the here linked section of this document.
At the moment of your request for password you will be inserted in a user mailing list that I will use to communicate new updates of the programs. You can be unsubscribed at any moment…

A short story of this idea

I came to the idea of writing STEM_CELL in 2004 when I was tired of writng many matlab script which could hardly talk with each other and were dispersed everey where in my hard disk. My discovery was that in EM simulation and analysis you have to do similar operation in many different circumstances.
I started with a C++ program based on the nice Kylix IDE-compiler which permitted to develop rapid graphic applications in quite the same way I was used to in Borland  C++ for windows. Linux was an ideal environment for long simulations and for c++ programming. In my case STEM_CELL was born to dialogate with the Kirkland routines. Unfortunately the kylix project has now been abandoned … I therefore migrated my project to windows that, unfortunately, does not integrate so well with long simulations.
Meanwhile many things have happened since I have written a parallel version of the Kirkland routines to simulate the HAADF images and I am migrating this project to large cluster for which the graphical interface cannot be directly applied.
I have used in this years STEM_CELL to create and test new analysis methods still not completeluy published , it is  therefore natural that part of the project is not totally freely available. Meanwhile I think that I can share important algorithms like GPA that would be otherwise obtained as comercial software.
Other parts will be soon made available and in particular the peak-pair analysis and the MEM filter for the STEM images.

Before download

The program STEM_CELL has been tested successfully on both Windows XP and Vista but should be in principle compatible with all previous versions of windows. Alas on windows Vista important isssue may come on the read only protections on many  folders built in Vista.
During the installation of STEM_CELL you will be asked to select a few folder, it is important that in all cases you grant a full access to these directories by changing the appropiate properties of the folders.
Alternatively the program can be installed outside the usual C/programs partitions in a location which is not system reserved.

The code is portected by GPL

 

Download

You can dowload the installer or the update the for free by subscribing at this site (register).

The upgrade is a copy of the executable file stem_cell.exe that must be substituted to the old executable with the same name in the correct folder.

Upgrades are of 2 kinds : default  and optimized

Normally optimized is better ( faster) but default provides more compatibility for example on mac user with emulation or wine.

I would like to ask you not to spread the software  to collegues but to ask them to subscribe, so that I can have track of all users.
This is usefull for statistical reasons and to comunicate you on important updates (it is not a SPAM list : typically  less than 1 mail in a month).

Installation instructions

The file install.exe is a self extracting executable so you shoul not have problem to install it. However newer system (Vista and win7 ) may have some permission issues when  acessing system folders. In this case you may want to try another installation an database directory outside the system tree , this usually solves the problems.

For sake of simplicity the program also ships in your installation dirctory a compile of kirkland code and an old version with very few changes.

The appropiate setting of environmental variables necessary to start simulation from with STEM_CELL is performed automatically with the new installation software so if you have a version <2.3.1.3 download the setup.exe and reinstall from scratch. Moreover to actvate the environmetal setting it can be necessary to restart  your PC.

Feel free to contact me for information and help

NOTE: Some users have experienced problems on notebooks with very low number of pixels (minimum pixel 650 x 900).
Linux user see FAQ

Manuals

A basic manual is  available for a few basic functions.

The single applications will soon have their own manual:

Manuals Video tutorials

STEM STRAIN equation solver [4,6]
Howie and Wehlan equation solver
STEMCELL under LINUX (WINE)
 

SUPERCELL manipulation+ simulationGPA

 Related Articles

MAIN ARTICLE regarding STEM_CELL

V. Grillo, E Rotunno
STEM_CELL: a software tool for electron microscopy. Part I Simulations
Ultramicroscopy (2012), http://dx.doi.org/10.1016/j.ultramic.2012.10.016

V. Grillo, F. Rossi
Ultramicroscopy (2012) STEM_CELL: A software tool for electron microscopy. Part2 analysis of crystalline materials
Ultramicroscopy (2012), http://dx.doi.org/10.1016/j.ultramic.2012.10.009

EXAMPLE of STEMCELL for GPA analysis

[1] S. D’Addato,  V. Grillo, S. Altieri, R. Tondi, S. Valeri and S. Frabboni
XPS and HR-TEM characterization of Nickel/Nickel Oxide core-shell nanoparticles
J. Phys.D: Condens. Matter 23 (2011)

[2] R. Buonsanti et al.(grillo)
Architectural Control of Seeded-Grown Magnetic-Semicondutor Iron Oxide-TiO2Nanorod Heterostructures: The Role of Seeds in Topology Selection
J. Am. Chem. Soc, 132 (2010) 2437–2464 http://dx.doi.org/10.1021/ja910322a

[3] D. Ercolani et al.(grillo)
InAs/InSb nanowire heterostructures grown by chemical beam epitaxy
Nanotechnology 20 (2009) 505605

STEMCELL simulations

[4] Grillo V.
The effect of surface strain relaxation on HAADF imaging
Ultramicroscopy 109(2009) 1453
http://dx.doi.org/10.1016/j.ultramic.2009.07.010

[5] Grillo et al.
On the influence of the static atomic displacement on atomic resolution Z-contrast imaging Phys.Rev. B 77 (2008), 054103

[6] V.Grillo F.Rossi
A new insight on crystalline strain and defect features by STEM- ADF imaging
J.Cryst .Growth 318(2011) 1151

[7] Carlino, E.; Grillo, V.; Palazzari, P.
Accurate and Fast Multislice Simulations of HAADF Image Contrast by Parallel Computing
Microscopy of Semiconducting Materials 2007, Springer Proceedings in Physics, Volume 120.ISBN 978-1-4020-8614-4. Springer Netherlands, 2008, p. 177
http://dx.doi.org/10.1007/978-1-4020-8615-1_38

[8] Carlino E, Grillo V
Atomic resolution stem-HAADF imaging in the study of interfaces
ARCHIVES OF METALLURGY AND MATERIALS 51, 23 (2006)
(can be downloaded here )

Probe deconvolution

[9] Grillo V.Microscopy and Microanalysis, vol. 17, issue S2, pp. 1292-1293

General references on geometric phase analysis

[10] M.Hytch et al.
Quantitative measurement of displacement and strain fields from HREM micrographs
Ultramicroscopy 74 (1998) 131 146

  • General references on simulation

[11] E.J.Kirkland
Advanced computing in Electon microscopy

 

 

 

FAQ

Q: Can I share this program with the people of my lab?
A: In principle the program is free but I would rather prefer an individual subscription on the download link.

Q: Shall I include you as a co-author in my articles?
A: Only if you require my scientific interaction or an articulated collaboration. In all other situations you are only required to cite one of my related works or this web-site.

Q: How can I get you parallel computing HAADF simulation
A: Actually at the moment you cannot… on a long term I am planning to make it free but for the moment I still need to publish a few results based on it. Nevertheless i can collaborate to produce specific results. If very large simulation are required it could be necessary to make a project or to allocate some money to pay machine time on the CINECA cluster I am using for simulations.  I also suggest you to use for small simulations the Kirkalnd routines that can be freely downlaoded and  with little effort, interfaced with STEM_CELL. I will distributre a partially modified version (with sources ) relatively soon under GPL licence.

 

Q: Can I install STEM_CELL under linux?
A: The best solution I have found is to install wine and then install STEM_CELL … However some problem usually arise: 1) grayscale images are deformed (set the appropiate options to solve this) 2) standard directory cannot be set ( some workaround can be easily made if you know how to set them under wine/linux). If you really need STEM_CELL under linux let me know.
Alternatively a native buggy and incomplete kylix version can be installed but i discontinued it a lot of time ago.

 

Q: Why there is a button with a bee?
A: It’s not a bee !!!, it is a “wasp” and is used for “swap” … soo you see the anagram … use this button to swap quadrant in fft representation.

 

Q: How can I get informed of your latest update ?
A:One way is to subscribe to STEM_CELL facebook page http://www.facebook.com/StemCellSoftware.

In order to avoid spam I rarely communivcate through the subscription email if not for crucial update.

NEW !!! With a version > 2.3.6.0  You can also watch  in
Extra->About
and you will know what is the newest version online.