Detailed Information on Publication Record
2015
Derivation of human induced pluripotent stem cells and Advanced Methods of Image Processing
KRONTORÁD KOUTNÁ, Irena, Pavel ŠIMARA, Pavel MATULA, Lenka TESAŘOVÁ, Barbara ŠALINGOVÁ et. al.Basic information
Original name
Derivation of human induced pluripotent stem cells and Advanced Methods of Image Processing
Name in Czech
Příprava lidských indukovaných kmenových buněk a pokročilé metody zpracování obrazu
Authors
KRONTORÁD KOUTNÁ, Irena (203 Czech Republic, guarantor, belonging to the institution), Pavel ŠIMARA (203 Czech Republic, belonging to the institution), Pavel MATULA (203 Czech Republic, belonging to the institution), Lenka TESAŘOVÁ (203 Czech Republic, belonging to the institution) and Barbara ŠALINGOVÁ (703 Slovakia, belonging to the institution)
Edition
CEITEC PhD Retreat, 23-24.4.2015, Valtice Czech Republic, 2015
Other information
Language
English
Type of outcome
Vyžádané přednášky
Field of Study
10600 1.6 Biological sciences
Country of publisher
Czech Republic
Confidentiality degree
není předmětem státního či obchodního tajemství
RIV identification code
RIV/00216224:14330/15:00081082
Organization unit
Faculty of Informatics
Keywords (in Czech)
iPSC; ESC;zpracování obrazu
Keywords in English
iPSC; ESC; Image processing
Změněno: 28/4/2016 20:29, RNDr. Pavel Šmerk, Ph.D.
V originále
Human induced pluripotent stem cells (hiPSCs) possess a great potential for clinical application. Various reprogramming techniques were presented during 7 years of hiPSCs research. Genome non-integrating and completely xeno-free protocols from the first biopsy to stable hiPSCs clones are highly preferable in terms of future clinical application. In CBIA lab we successfully generated hiPSCs using STEMCCA lentivirus, Sendai virus or episomal vectors. Human fibroblasts and CD34+ blood progenitors were used as a source cells and were maintained either on mouse embryonic feeder cells or in feeder-free conditions. The reprogramming efficiency was comparable for all three methods and both cell types, while the best results were obtained in feeder-free conditions. The pluripotency of our hiPSCs was verified by differentiation into all three germ layers and by teratoma assay. In order to study genomic integrity, we monitored DNA damage response (DDR). Image analysis of imunohistochemical or ImunoFISH experiments is very important step of iPSCs evaluation in the context of their genome integrity and stability. In CBIA lab was develop unique software “Acquiarium” for this advanced image analysis. Acquiarium is open source software (GPL) for carrying out the common pipeline of many spatial cell studies using fluorescence microscopy. It addresses image capture, raw image correction, image segmentation, quantification of segmented objects and their spatial arrangement, volume rendering, and statistical evaluation. It is focused on quantification of spatial properties of many objects and their mutual spatial relations in a collection of many 3D images. It can be used for analysis of a collection of 2D images or time lapse series of 2D or 3D images as well. It has a modular design and is extensible via plug-ins. It is a stand-alone, easy to install application written in C++ language. The GUI is written using cross-platform wxWidgets library.
In Czech
Human induced pluripotent stem cells (hiPSCs) possess a great potential for clinical application. Various reprogramming techniques were presented during 7 years of hiPSCs research. Genome non-integrating and completely xeno-free protocols from the first biopsy to stable hiPSCs clones are highly preferable in terms of future clinical application. In CBIA lab we successfully generated hiPSCs using STEMCCA lentivirus, Sendai virus or episomal vectors. Human fibroblasts and CD34+ blood progenitors were used as a source cells and were maintained either on mouse embryonic feeder cells or in feeder-free conditions. The reprogramming efficiency was comparable for all three methods and both cell types, while the best results were obtained in feeder-free conditions. The pluripotency of our hiPSCs was verified by differentiation into all three germ layers and by teratoma assay. In order to study genomic integrity, we monitored DNA damage response (DDR). Image analysis of imunohistochemical or ImunoFISH experiments is very important step of iPSCs evaluation in the context of their genome integrity and stability. In CBIA lab was develop unique software “Acquiarium” for this advanced image analysis. Acquiarium is open source software (GPL) for carrying out the common pipeline of many spatial cell studies using fluorescence microscopy. It addresses image capture, raw image correction, image segmentation, quantification of segmented objects and their spatial arrangement, volume rendering, and statistical evaluation. It is focused on quantification of spatial properties of many objects and their mutual spatial relations in a collection of many 3D images. It can be used for analysis of a collection of 2D images or time lapse series of 2D or 3D images as well. It has a modular design and is extensible via plug-ins. It is a stand-alone, easy to install application written in C++ language. The GUI is written using cross-platform wxWidgets library.
Links
| GBP302/12/G157, research and development project |
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