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

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

(Replace FILENAME)

=> URL = http://beta.cytomine.be/#tabs-image-PROJECT-IMAGEINSTANCE-

StandardSample
 
Sample (cytomine-dev ; 10.19.5.34)ID image instanceURL
TIFF pyramidal(tick)

/var/images/TIFF/_NEO4_HPg_INH_8.7001.tif.vips.tif

/var/images/TIFF/OC_CD31_04840029C0001S_converted.tif

/var/images/TIFF/out_final_52_36__overlap_0_0_w1_vips.tif

1676http://beta.cytomine.be/#tabs-image-57-1676-
TIFF planarTIFF   
PNG

TIFF

   
PGMTIFF   
JPEGTIFF   
JPEG2000(tick)/var/images/JPEG2000/PGP_POUMON_PBS_3_21_-_2012-08-08_11.07.24.jp27889452http://beta.cytomine.be/#tabs-image-7873585-7889452-
BMPTIFF   
AdvancedSampleSample (cytomine-dev ; 10.19.5.34)ID image instanceURLRemarks
SVS Aperio

(tick)

(tick)

/var/images/SVS/BM_GRAZ_HE_0016.svs

/var/images/SVS/BM_GRAZ_HE_0035.svs

100117637

140857517

http://beta.cytomine.be/#tabs-image-93519082-100117637-

http://beta.cytomine.be/#tabs-image-140835231-140857517-

encoding compression JP2K YCBCR

encoding JPEG

NDPI Hamamatsu(tick)/var/images/NDPI/BABL_2_-_2014-12-04_10.11.50.ndpi150090604http://beta.cytomine.be/#tabs-image-150079801-150090604- 
VMS Hamamatsu(tick)/var/images/VMS/11H10260_LBA_Papa_-_2012-01-26_14.25.48_clip.vms377590http://beta.cytomine.be/#tabs-image-65-377590- 
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.mrxs142212708http://beta.cytomine.be/#tabs-image-101903411-142212708- 
TIFF Philips     
SVS Sakura(tick)/var/images/SVS/10B01380_C4_DIV_-_2013-01-17_10.37.01.svs14696089http://beta.cytomine.be/#tabs-image-14691185-14696089- 
TIFF ventana(tick)/1411647998215/7fc4924b-455b-4190-8fb5-6fad2644fce7.vtif
/var/images/VTIFF/910cf3c7-5f54-457c-96f9-f9f8e19380eb.vtif
137879263
706 (aurora)
http://beta.cytomine.be/#tabs-image-92279388-137879263- 
BIFF ventana     
CZI Zeiss    No direct support but indirect through TIFF conversion with CZI Converter (parameters: BigTIFF, no pyramid, no attachment images): http://hcbi.fas.harvard.edu/resources_software

 

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.

 

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