In [8]:

    

import sys, os
print 'Working in %s' % os.path.abspath(os.path.curdir)

# adding path to python modules
sys.path.append('../src/python')

import pmip;
import aibs;
reload(pmip); reload(aibs);


    

    




Working in /vagrant/notebooks

In [3]:

    

api = aibs.api()


    

In [4]:

    

explist = api.getValidSpecimentsWithName('H08-0083.01')

e = explist[0]

e.markersOfInterest = ['PCP4']
e.getMarkerList(verbose=False)
e.getSectionImages()


    

    
Out[4]:





[006-100034525 - [ 23552 x 16896 ],
 036-100034525 - [ 24256 x 18624 ],
 066-100034525 - [ 24256 x 20639 ],
 096-100034525 - [ 26048 x 20575 ],
 126-100034525 - [ 25344 x 21375 ],
 156-100034525 - [ 25344 x 20864 ],
 186-100034525 - [ 25536 x 21312 ],
 216-100034525 - [ 25311 x 20992 ],
 246-100034525 - [ 25216 x 20031 ],
 276-100034525 - [ 25664 x 19583 ]]

In [5]:

    

e.filteredMarkers


    

    
Out[5]:





[{'id': 100034525, 'name': u'PCP4', 'type': 'ISH'}]

In [6]:

    

e.metadata


    

    
Out[6]:





{u'chemotherapy': None,
 u'donor_id': 1345,
 u'egfr_amplification': None,
 u'extent_of_resection': None,
 u'external_specimen_name': None,
 u'hemisphere': u'(none)',
 u'id': 4350,
 u'mgmt_pcr': None,
 u'name': u'H08-0083.01',
 u'parent_id': None,
 u'parent_x_coord': None,
 u'parent_y_coord': None,
 u'parent_z_coord': None,
 u'pten_deletion': None,
 u'radiation_therapy': None,
 u'rna_integrity_number': 6.9,
 u'smoker': None,
 u'specimen_id_path': u'/4350/',
 u'structure_id': 1157,
 u'tissue_ph': None,
 u'tumor_status': None}

In [7]:

    

e.printSpecimenDetails()


    

    




all markers
[{'id': 100034619, 'name': u'SST', 'type': 'ISH'},
 {'id': 100030029, 'name': u'RORB', 'type': 'ISH'},
 {'id': 100034641, 'name': u'VIP', 'type': 'ISH'},
 {'id': 100033518, 'name': u'NTNG2', 'type': 'ISH'},
 {'id': 100032212, 'name': u'PRKCB', 'type': 'ISH'},
 {'id': 100033402, 'name': u'NDNF', 'type': 'ISH'},
 {'id': 100034539, 'name': u'CXCL14', 'type': 'ISH'},
 {'id': 100029767, 'name': u'NISSL', 'type': 'HIS'},
 {'id': 100029915, 'name': u'PVALB', 'type': 'ISH'},
 {'id': 100030581, 'name': u'FOXP2', 'type': 'ISH'},
 {'id': 100034580, 'name': u'PDE1A', 'type': 'ISH'},
 {'id': 100032506, 'name': u'CALB2', 'type': 'ISH'},
 {'id': 100032306, 'name': u'MBP', 'type': 'ISH'},
 {'id': 100029918, 'name': u'CALB1', 'type': 'ISH'},
 {'id': 100035174, 'name': u'SYNPR', 'type': 'ISH'},
 {'id': 100034871, 'name': u'NRXN1', 'type': 'ISH'},
 {'id': 100034612, 'name': u'RELN', 'type': 'ISH'},
 {'id': 100034759, 'name': u'GAD1', 'type': 'ISH'},
 {'id': 100035059, 'name': u'AIF1', 'type': 'ISH'},
 {'id': 100034306, 'name': u'VAT1L', 'type': 'ISH'},
 {'id': 100034327, 'name': u'CTGF', 'type': 'ISH'},
 {'id': 100034525, 'name': u'PCP4', 'type': 'ISH'},
 {'id': 100030594, 'name': u'CNTNAP2', 'type': 'ISH'},
 {'id': 100034531, 'name': u'SLC1A2', 'type': 'ISH'},
 {'id': 100029764, 'name': u'MFGE8', 'type': 'ISH'}]
filtered markers
[{'id': 100034525, 'name': u'PCP4', 'type': 'ISH'}]
section image list
[006-100034525 - [ 23552 x 16896 ],
 036-100034525 - [ 24256 x 18624 ],
 066-100034525 - [ 24256 x 20639 ],
 096-100034525 - [ 26048 x 20575 ],
 126-100034525 - [ 25344 x 21375 ],
 156-100034525 - [ 25344 x 20864 ],
 186-100034525 - [ 25536 x 21312 ],
 216-100034525 - [ 25311 x 20992 ],
 246-100034525 - [ 25216 x 20031 ],
 276-100034525 - [ 25664 x 19583 ]]

In [ ]: