uu.seUppsala universitets publikasjoner
Endre søk
RefereraExporteraLink to record
Permanent link

Direct link
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Annet format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annet språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf
Viewing and analyzing slide scanner data using CellProfiler (work in progress)
Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion. (Wählby lab)
Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion. (Wählby lab)
Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion. Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, MA, USA. (Wählby lab)
2013 (engelsk)Inngår i: European BioImage Analysis Symposium 2013 / [ed] Julien Colombelli, 2013, s. 58-Konferansepaper, Poster (with or without abstract) (Annet vitenskapelig)
Abstract [en]

Viewing and analyzing slide scanner data using CellProfiler (work in progress)

Petter Ranefall1, Alexandra Pacureanu1, and Carolina Wählby1,2

1Centre for Image Analysis, Department of Information Technology, Uppsala University, and Science for Life Laboratory, Sweden

2Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, MA, USA

 

The amount of image data in a slide scanner image is usually very large, inducing challenges for image analysis and visualization. We would like to use the strengths and flexibility of CellProfiler for the image analysis, but performing high-resolution image analysis on large slide scanner images is unfortunately not possible due to memory limitations. At the same time, we would like to visualize the results of the analysis in the context of the full tissue slide so that for example phenotypic variations at the sub-cellular level can be related to lower-resolution structures such as vessels, ducts, or tumors in the tissue.

 

To approach this problem we split the image into smaller tiles that are more suitable for CellProfiler to handle. By keeping track of the coordinates of the tiles we can display the results on the original, full-size image. Our aim is to enable visual examination at multiple resolutions and with the option to toggle results such as segmentation masks and classification results on or off using a “Google Maps” type of view.

 

In particular, we work with tissue profiling by in situ sequencing of RNA molecules. The tissue samples have to be removed from the microscope for each new sequencing cycle. In this case, and in other applications dealing with repeated staining, there are often differences in the alignment between the imaging rounds. We assume that these misalignments are rigid (only translation and rotation), and we have added an image registration step in order to align the different channels before partitioning the images into tiles suitable for analysis in CellProfiler. 

sted, utgiver, år, opplag, sider
2013. s. 58-
HSV kategori
Forskningsprogram
Datoriserad bildanalys
Identifikatorer
URN: urn:nbn:se:uu:diva-209613OAI: oai:DiVA.org:uu-209613DiVA, id: diva2:658701
Konferanse
European BioImage Analysis Symposium 2013, Barcelona
Tilgjengelig fra: 2013-10-22 Laget: 2013-10-22 Sist oppdatert: 2013-10-30bibliografisk kontrollert

Open Access i DiVA

Fulltekst mangler i DiVA

Av organisasjonen

Søk utenfor DiVA

GoogleGoogle Scholar

urn-nbn

Altmetric

urn-nbn
Totalt: 557 treff
RefereraExporteraLink to record
Permanent link

Direct link
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Annet format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annet språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf