mainMicroscopePictureStitch - Summary

 
 
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Id: #647
System Name: mipisti
Name: MicroscopePictureStitch
Group Type: Programs

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<BR> <I> T_a_k_e__c_a_r_e__o_f__y_o_u_r__R_I_G_H_T_S.<BR> _P_r_e_v_e_n_t__L_O_G_I_C--P_A_T_E_N_T_S_<BR>(alias softwarepatents, computer embedded patents).<BR> http://www.ffii.org, http://www.nosoftwarepatents.org </i> <BR>

<H1>Stitching a large number of Microscope Pictures </h1>
Suppose you want to analyse an object with your microscope which is much too big for one photo. Several programs offer to arrange charts to one overall picture. But very often those programs are not accurate enough (they may change scaling / orientation) and configuration is limited. These programs are not specialized for processing microscope pictures. That was the reason for me to develop my own microscope picture stitching program :-)

MiPiSti is designed for this purpose only. The idea is (already working with 24BPP-RGB and 8BPP-greyscale BMP-files) that you have a sequence of (pairwise) overlapping pictures (see http://home.gna.org/mipisti/ for details).

MiPiSti works in 2 steps. In the first step, mipisti calculates the offset position of each picture and its successor in the sequence of pictures. In the second step those offsets are used to put all pictures into one overall picture. It is planned, that image correction (lens errors (dust...) inhomogeneous illumination) will be done in this step as well (see task-tracker for details).

Basic functions work stable (with 24Bit uncompressed BMP). The command line program ("bmp" or "fast") can calculate offsets and stitch a sequence of bmp-files as well as putting a scaling into the picture. There are scripts available to do automatic stitching.

<H2> A first <B>GUI</b> is finished. </h2>
There are 3 GUI-programs: adjust.tcl, readjust.tcl and scale.tcl - as well as 1 command-line-programm: fast. You find Win-executables in the bin-directory.
<B>adjust.tcl</b> is a frontend for the command-line-program fast.
<B>readjust.tcl</b> is for correcting errors in the mergelist.
<B>scale.tcl</b> if for putting a scale into a bmp-picture.

I admit, those first GUIs are not too nice, but they do their job.
I use the programs to automatically stitch more than 500 particular pictures of 640x400 24BPP-RGB BMP, without problems.

On the other hand, there are advantages of the underlying algorithm:

  • while calculating offsets, only 2 pictures are held in memory independent of overall number of particular pictures
  • calculating time is linear to the number of particular pictures
  • the number of random-test-points and the overlap-minimum can be controlled (accuracy <-> speed), iteration/adaption is possible
  • all intermediate informations (offsets, quality ...) are stored as ASCII-data
  • everything can be controlled via batch/command-line or GUI (Tcl/Tk)

Using the sources, you need a Tcl/Tk interpreter (free http://www.tcl.tk) Img-lib and a C++ compiler like gcc (mingw) to compile <i>"fast"</i>. They work on Debian, SuSE, Win2k/XP and hopefully on all Tcl/Tk && gcc supported platforms like BSD, Mac, Win9x ...

A daily CVS-source-snapshot can be downloaded:
http://cvs.gna.org/daily/mipisti-snapshot.tar.gz.

Registration Date: Sun 27 Jun 2004 09:42:40 PM UTC
License: GNU General Public License V2 or later
Development Status: 5 - Production/Stable

 

Latest News 
New Feature: Diagramm-Analysis
     posted by trebor, Thu 08 Jun 2006 12:36:52 PM UTC - 0 replies

A picture of a diagram now can analyzed, resulting in a csv-file containing informations for curves which are discriminated by color (so maybe one needs to colorize them first (via gimp)).
The command -DiagAnalyze allows linear as well as logarithmic scaled y-axis and linear scaled x-axis (till now) to be analyzed. ...


[Read more]
Files are SIGNED now
     posted by trebor, Sat 08 Apr 2006 04:53:32 PM UTC - 0 replies

All files in the download-area are signed via gpg.
There is a GUI for signing files in directories recursively. It works with gpg-agent. You can download it in the tclittle project-cvs.

New Version 0.9.3
     posted by trebor, Fri 04 Mar 2005 01:18:00 PM UTC - 0 replies

Windows binaries are in download/bin.

New Buttons:

  • goto q

only change stitching of lower quality

  • configure

change configuration while adjusting, save configuration to file

  • old value

reset to old values

Windows Binaries in Download-Area
     posted by trebor, Wed 02 Mar 2005 11:54:21 AM UTC - 0 replies

There are 3 windows executables in the download-area (directory bin):
adjust_wrap.exe
readjust_wrap.exe
scalewrap.exe.

They all need write acces inside their directory/location, because they always unpack fast.exe and font1.txt there.


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