CELLmicrocosmos 5
CellVisualization

  • Pre-Release: 14.03.2014
  • changes
  • The Source Code will be published after the first full publication.
  • The documentation is not
    completely finished by now!
  • Find info about current updates
    (Last Update: 14.03.2014)
  • Learn about the infrastructure
  • Problems & Solutions
  • The Online Version has been published! Read more!
  • Or learn about all
    associated publications
    in
    JIB 2010 or in BIOSTEC 2010.
  • Thanks go to
    team.CELLmicrocosmos.org
  • Based on Blender

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Pre-Release Info

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Databases

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  • Visualize 2D networks based on the selected localizations
  • Map the generated networks into a 3D cell environment (based on the Cm1 project)
  • Export cell models in VRML97
  • Supports Stereoscopic 3D Visualization for professional Graphic Cards (e.g. NVIDIA Quadro FX) or regular monitors in side-by-side format

JCBC Article 2013

Team

  Find the original starting page here.

Workshops

All Cell Visualization projects presented here started with workshops presented to my students, one important focus here is Bio Visualization with Blender. Here, we are listing some workshops we presented in the past. If you are interested in workshops - for teaching or conferences - please feel free to contact us: This email address is being protected from spambots. You need JavaScript enabled to view it.

2018

Bio Visualisation with Blender and MembraneEditor, Konstanz Research School Chemical Biology (KoRS-CB)

Tutors: Mehmood Ghaffar, Bjorn Sommer

2017

BioVis Mini Workshop, Integrative Bioinformatics Conference in Odense 2017  

Tutors: Mehmood Ghaffar, Bjorn Sommer

2016

BioVis Workshops, VizBi 2016 in Heidelberg

Tutors: Chris Hammang, Bjorn Sommer

WS2014-2015

CELLmicrocosmos Cell Visualization, Bielefeld University (Student Project) 

Tutors: Niklas Biere, Bjorn Sommer

WS2013-2014

CELLmicrocosmos Cell Modeling, Bielefeld University (with Blender, Student Project)

Tutor: Bjorn Sommer

SS 2013

CELLmicrocosmos Cell Modeling, Bielefeld University (with Blender, Student Project)

Tutor: Bjorn Sommer

 

 

CELLmicrocosmos

5

CellVisualization

changes

  • Graphical modeling of cells by using Blender
  • Interpretation of microscopic data
  • 3D Segmentation using Fiji
  • Stereoscopic 3D Rendering for 3D TVs, VR Cardboards as well as professional solutions like 3D Cinema or Power walls

Watch out for News

Find info about current updates 
(Last Update: 17.07.2018)

Watch the 3D Videos!

 

 

 

 

 
 

Watch it in 3D or 2D

 
  • A bunch of videos, old ones and new ones, are found here!
  • Two brand new publications are coming, the first one is out now!

Meet the Team!

 

 

 

 

 

Blender membrane scripts

Author: Mehmood Ghaffar

The membrane script can be used to create a 2D array of linearly distributed membrane patch. The script has already reduced a number of steps in this process, however, additional steps need to be taken to get the results as they are presented in the paper. This could be a tediuos job, as it require some baisc skills of Blender suite.

This work will be presented at the VINCI 2018 in Växjö, Sweden (13-15 August 2018):

Mehmood Ghaffar, Niklas Biere, Daniel Jäger, Karsten Klein, Falk Schreiber, Olaf Kruse and Björn Sommer: 3D Modelling and Visualisation of Heterogeneous Cell Membranes in Blender

Getting started with the membrane script will require the following steps.

a) Installing creaprim Plugin:

To create a list of custom objects, a plugin "creaprim" is required. The file creaprim.py can be downloaded from the download section and can be distributed freely under GNU license.

Download

Please download the required files in this ZIP archive:

Blender Membrane Script, M. Ghaffar (v. 1.0)

Steps for 'CreaPrim' Plugin Installation

  1. Download the "creaprim.py" file and keep it in some easy accessible place such as "C:\Downloads".
  2. Start Blender suite.
  3. From File menu, select "User Preferences".
  4. Click on "Install Add-on from File".
  5. Choose "creaprim.py" from "C:\Downloads" and press Enter or click "Install Add-on from File" button.
  6. Click "Save User settings".
  7. "CreaPrim" should appear in the Tools section in the left of the Blender User Interfaces.
  8. Create/model some objects in the scene and give them proper names.
  9. Select all the objects and give them a name 'myList' inside CreaPrim user interface in the left side. 
  10. Click "Create primitive" button inside CreaPrim Panel.

To check your new list of self created objects, click Add -> Mesh -> myList

The required Lipid models in the thylakoid membrane can be found in All_models.blend file

Installing and running the membrane plugin:

Follow these steps to run membrane script.

  1. Open Blender
  2. Change view to Scripting mode.
  3. Click open in the editor on the left side of the view.
  4. Select membraneScript.txt and click ok
  5. Click Run Script
  6. Go to the properties panel on the right of the 3D view. (press N to show the panel)
  7. If you see "My Panel", congratulations to you. You have successfully load the script.

Getting started with the membrane script

Note: The plugin is not yet stable but workable if certain conditions are pre considered.

please follow the following guidelines to enjoy smooth experience.

  1. Before clicking the Run Script button, make sure the scene is emtpy. To delete all objects from the scene, Press 'A' twice to select everything and then press 'X' + ENTER to delete all objects.
  2. Click 'Run Script' button.
  3. From My panel, click 'Add' to create a 2D surface.
  4. Select an appropriate subdivision no in the next field.
  5. Choose, how many lipid types you want to insert into this 2D surface.
  6. Give percentage for each and individual lipid type.
  7. Hit create button.
  8. At this stage, you have successfully divided 2D surface into custom no. of sub surfaces which are randomly distributed.
  9. Apply colors from the available color schemes to see how your membrane patch would look like.
  10. If you are not happy with the current pattern of random distribution of sub surfaces, you can change it via seed no.
  11. Click on the seed no. and change it to see another pattern.
  12. Once you are done with the pattern. click Enable Lipid Packing mode.
  13. This section is tedious as you have to do some manual work.
  14. Load all the lipids from the custom menu of lipid lists.
  15. Select each sub surfaces and replace the percentage with the name of lipid you want to assign to that particular surface.
  16. Click Assign Lipids
  17. Go to object properties, the cube on the right side properties section.
  18. Select Faces under the duplication.
  19. Repeat for all other remaining sub surfaces.
  20. In the end you will come up with a nicely looking randomly mixed pattern of lipids.

 

Cm5 Publications

Journal Articles

Biere, Niklas; Ghaffar, Mehmood; Doebbe, Anja; Jäger, Daniel; Rothe, Nils; Friedrich, Benjamin M.; Hofestädt, Ralf; Schreiber, Falk; Kruse, Olaf; Sommer, Björn: Heuristic Modeling and 3D Stereoscopic Visualization of a Chlamydomonas reinhardtii Cell. Journal of Integrative Bioinformatics, 15(2), 2018, DOI: https://doi.org/10.1515/jib-2018-0003.

Sommer, Björn; Bender, Christian; Hoppe, Tobias; Gamroth, Chrstian; Jelonek, LukasStereoscopic cell visualization: from mesoscopic to molecular scale. Journal of Electronic Imaging, 23(1), 2014, DOI: https://doi.org/10.1117/1.JEI.23.1.011007.

Conference Articles

Ghaffar, Mehmood; Biere, Niklas; Jäger, Daniel; Klein, Karsten; Schreiber, Falk; Kruse, Olaf; Sommer, Björn: 3D Modelling and Visualisation of Heterogeneous Cell Membranes in Blender. In Proceedings of VINCI'18, 2018, DOI: https://doi.org/10.1145/3231622.3231639.

Please also check the blender membrane scripts section!

Abstracts

Biere, Niklas; Doebbe, Anja; Rothe, Nils; Thomas Huser, Kruse, Olaf; Sommer, Björn: Towards a 3D Cell Model of Chlamydomonas reinhardtii (Workshop Abstract). In Proceedings of the CELLmicrocosmos neXt workshop, 2014.

Videos

Here, you will find all videos created in the context of the CELLmicrocosmos project.

Further videos will follow, so watch out for our CELLmicrocosmos channel on YouTube!

Chlamydomonas 3D - From Biological Cells to Biofuels

The video shows how the green algae cell Chlamydomonas rheinhardtii can be used to create fuel. It discusses the underlying processes by making use of stereoscopic 3D visualization. The complete video was modeled and rendered with the free Open Source software Blender. Cutting was done by using Lightworks.

The video is discussed in the publication:
"Heuristic Modeling and 3D Stereoscopic Visualization of a Chlamydomonas reinhardtii Cell"
https://doi.org/10.1515/jib-2018-0003

This video won the Best-of-Show in Animation/CG at the Stereoscopic Displays and Applications Conference in 2016:
http://stereoscopic.org/3dcinema

Tools: Blender, Lightworks 12

Production year: 2015-18

(3D 4K for 3D 4K-TVs) [version 1.2.1]

(3D for 3D HD-TVs) [version 1.2.1]

(Anaglyph 3D for Red/Cyan Glasses) [version 1.2.1]

(2D) [version 1.2]

CELLmicrocosmos Cell Modeling SS 2012

This is an educational 3D video from 2014 done by two students who were new to Blender. Here, in some scenes, mistakes were made in terms of Stereoscopic 3D Visualization. These mistakes as well as the positive aspects were discussed in the associated publication: "Stereoscopic Cell Visualization: From Molecular to Mesoscopic Scale" from 2014: https://doi.org/10.1117/1.JEI.23.1.011007

Tool: Blender

Production year: 2013

Animation Bachelor Thesis Sommer 2003

Tools: Autodesk 3DS Max version 5-7

Production year: 2003

For historical reasons ;-) coming soon ...

Other Animations

A cardiomyopathy-related nsSNP Network localized with CmPI 3D

This visualization was done in context of a localization for a publication. The subcellular localization is based on the databases UniProt, GO, Reactome (contained in the data warehouse DAWIS-M.D.).

The cell model was created with CmPI (CELLmicrocosmos Pathway Integration) and then rendered with Blender. It is supplementary material for the publication:
http://doi.org/10.1074/jbc.M115.695247 

This is a stereoscopic 3D movie!

Test Video Interdisciplinary Cell Visualization

This is a stereoscopic 3D movie!

Watch all videos directly at YouTube here:

http://www.youtube.com/user/CELLmicrocosmos