Page tree
Skip to end of metadata
Go to start of metadata

Request to find the image-instance id from the filename:

SELECT ii.project_id,, ai.filename
FROM abstract_image ai, image_instance ii
WHERE ii.base_image_id =
AND ai.filename like '%FILENAME%';

(Replace FILENAME)

=> URL =

Sample (cytomine-dev ; image instanceURL
TIFF pyramidal(tick)




TIFF planarTIFF   


AdvancedSampleSample (cytomine-dev ; image instanceURLRemarks
SVS Aperio







encoding compression JP2K YCBCR

encoding JPEG

NDPI Hamamatsu(tick)/var/images/NDPI/BABL_2_-_2014-12-04_10.11.50.ndpi150090604 
VMS Hamamatsu(tick)/var/images/VMS/11H10260_LBA_Papa_-_2012-01-26_14.25.48_clip.vms377590 
SCN Leica(tick)/var/images/SCN/40X_ImageCollection_0000000157_2013-03-27_16_12_31.scn?  
MRXS Mirax(tick)/var/images/SCN/CD56_noir_CD34_rouge.mrxs142212708 
TIFF Philips     
SVS Sakura(tick)/var/images/SVS/10B01380_C4_DIV_-_2013-01-17_10.37.01.svs14696089 
TIFF ventana(tick)/1411647998215/7fc4924b-455b-4190-8fb5-6fad2644fce7.vtif
706 (aurora) 
BIFF ventana     
CZI Zeiss    No direct support but indirect through TIFF conversion with CZI Converter (parameters: BigTIFF, no pyramid, no attachment images):


Image format architecture

All formats in Cytomine are in one of these categories :

  • Natively supported;
  • Supported after a light conversion;
  • Supported after a heavy conversion (heavy means the conversion takes a long time).

Natively supported :

All the natively supported images extend the SupportedImageFormat class. Currently, we can natively support the following formats :

  • Pyramidal TIFF 
  • JPEG 2000
  • All the formats supported by OpenSlide. Thes formats are split into the SingleFile and MultipleFiles.

Supported after a light conversion :

One light convertor is VIPS to "pyramidalize" the non-pyramidal images. All formats of this category must implement the IConvertableImageFormat.

Example :

  • JPEG, PNG, BMP are common format that need to be "pyramidalized" with vips. 
  • PlanarTIFF, HuronTIFF , etc. are tiff not recognized by iipsrv that need to be converted by vips. It takes few second. ==> Light conversion.

Supported after a heavy conversion :

One heavy convertor is BioFormat. All format convertable (to TIFF) by BioFormat extends BioFormat class and implement the IHeavyConvertableImageFormat.


  • No labels