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 Orchestration of differentiation, migration and re-assembly of cells is one of the most fundamental aspects of pattern formation of tissues and organs, including central nervous system. We thought that these coordinated behaviors of cells are regulated by a genetic program, in which pivotal genes regulate these steps in a tight and precise manner. This also implies that careful dissection of this genetic program and detailed analyses of functions of genes should help us to understand complicated morphogenesis of tissues and organs. Nonetheless, we have just come to a point to re-evaluate our approaches and to proceed to a new field, which has never been explored.
 

Pattern formation, such as the Benard convection and the Taylor instability, is also extensively studied in physics and chemistry. In these cases, a homogenous group of molecules can form orderly patterns. In another case, oxidative and reductive states repeat in an oscillatory way, known as the (Belousov-Zhabotinsky) B-Z reaction. These indicate that autonomous mechanisms do exist even in developing embryos, some of which were already studied extensively by Turing and Meinhard.

 We have been exploring molecular mechanisms of pattern formation of vertebrate embryos, with central nervous system, limb bud and heart as model organs, and with several key transcription factors as our keen interest. Nonetheless, we have noticed that extensive analyses on the genetic programs are not sufficient for understanding thoroughly the dynamic pattern formation of developing embryos. Recently, we have identified that several proteins change their shapes and conformation in response to physical forces that are generated by cells, hereby such strains trigger next biochemical responses. We are now studying this novel mechanism to understand functional roles of physical forces generated by cells and sensed by cells.


Development of CT image analysis tools for mouse adipose tissues (BAT, WAT, Beige / Brite)

 

 In this research, we developed the program that is able to automatically carry out quantitative and qualitative image analysis of mouse adipose tissues (WAT, BAT, Beige/Brite) by using X-ray CT data.

 You can easily generate 2D and 3D images that have analysis accuracy of single-voxel (WAT: 21.7 cells per single-voxel, BAT: 123 cells per single-voxel). We will broadly provide these tools to wet-lab researchers.

Direction for use is 
HERE

Copyright acknowledgement
 Dr. Akihiro Nakaya also has a part of the copyright of this program. Please refer to Dr. Akihiro Nakaya (Niigata Univ.) and Keiko Ogura (IDAC., Tohoku Univ.) in any presentation at meetings and an article with images or graphs that you made with this program.



3D CT image analysis of adipose tissues (BAT~Beige/Brite~WAT) in mice (Improvement of OsiriXMarch 2015 Revision


We develop convenient color settings with OSS (Open Source Software) OsiriX to analyze Beige/Brite in mice. Just try using our settings !
*This software supports Mac OS 10.7 (Lion) and later.
*OsiriX supports the DICOM file formats.
*Exposure conditions HERE.

1. Use the link below to download the OsiriX for Mac ("Osirix5.6 .dmg)
http://www.osirix-viewer.com/OsiriX5.6.dmg

2.
Download color setting file (“mouse_Beige2.plist”) HERE !
*File → Save as …
*Do not change file extension.

3. Move the file (mouse_Beige2.plist) to (username)/Document/OsiriX/Data/CLUT.

4. Boot "OsiriX"

5. Select "3D Viewer"  →  "3D Volume Rendering"

6. Set mouse_Beige2 in CLUT pull-down menu.

7. Uncheck "shading" checkbox in upper menu.

* WAT → Red, Beige/Brite → Sky blue, BAT → Yellow, Muscle → Dark blue.

Copyright acknowledgement
Dr. Akihiro Nakaya also has a part of the copyright of this program. Please refer to Dr. Akihiro Nakaya (Niigata Univ.) and Keiko Ogura (IDAC., Tohoku Univ.) in any presentation at meetings and an article with images or graphs that you made with this program.

* Correspondence : keiko-o@idac.tohoku.ac.jp



3D CT image analysis of skeletal muscle of the lower leg in mice and ROI histgram analysis tool (Improvement of OsiriX )


We develop convenient color settings with OSS (Open Source Software) OsiriX to analyze skeletal muscles of the lower leg in mice (Soleus and Gastrocnemius).
*This software supports Mac OS 10.7 (Lion) and later.
*OsiriX supports the DICOM file formats.
*Exposure conditions HERE.

1. Use the link below to download the OsiriX for Mac ("Osirix5.6 .dmg)
http://www.osirix-viewer.com/OsiriX5.6.dmg

2.
Download color setting file (“mouse_Muscle1.plist”) and (“mouse_Muscle2.plist”)HERE!
*File → Save as …
*Do not change file extension.

3. Move the file (“mouse_Muscle1.plist”and “mouse_Muscle2.plist” ) to (username)/Document/OsiriX/Data/CLUT.

4. Boot "OsiriX"

5. Select "3D Viewer"  →  "3D Volume Rendering"

6. Set “mouse_Muscle1” or “mouse_Muscle2” in CLUT pull-down menu.

7. Uncheck "shading" checkbox in upper menu.

* mouse_Muscle1
 WAT → Red, BAT → Yellow, Muscle low → Pale pink, Soleus → Dark Blue, Gastrocnemius → Pink, Muscle middle → Light Blue, Muscle high → Green, Bone → white

* mouse_Muscle2
 WAT → Red, BAT → Yellow, Soleus → Dark Blue, Gastrocnemius → Pink, Muscle high → Green, Bone → white


You can also make the ROI histogram from input data using ROI select tool in OsiriX with our new tools HERE !

Copyright acknowledgement
Please refer to Keiko Ogura (IDAC., Tohoku Univ.) and Keisuke Izumi (GSIS., Tohoku Univ.) in any presentation at meetings and/or any article with images or graphs that you made with our program.

* Correspondence : keiko-o@idac.tohoku.ac.jp