Dependencies¶
In [1]:
import matplotlib
import numpy as np
import matplotlib.pyplot as plt
from idr import connection
matplotlib.rcParams['figure.figsize'] = (12.0, 8.0)
In [2]:
screen = "idr0001-graml-sysgro/screenA"
Connect to IDR¶
In [12]:
conn = connection()
Load information about Sysgro¶
In [3]:
idr0001 = [x for x in conn.listScreens(2) if x.name == screen][0]
In [4]:
idr0001.name
Out[4]:
u'idr0001-graml-sysgro/screenA'
In [5]:
print(idr0001.description)
Publication Title A Genomic Multiprocess Survey of Machineries that Control and Link Cell Shape, Microtubule Organization, and Cell-Cycle Progression Screen Description Primary screen of fission yeast knock out mutants looking for genes controlling cell shape, microtubules, and cell-cycle progression. 262 genes controlling specific aspects of those processes are identifed, validated, and functionally annotated.
In [11]:
annotations = idr0001.getAnnotation().getMapValueAsMap()
print("""
PubMed ID: %(PubMed ID)s
Authors: %(Publication Authors)s
Imaging Method: %(Imaging Method)s
""" % annotations)
PubMed ID: 25373780 http://www.ncbi.nlm.nih.gov/pubmed/25373780 Authors: Graml V, Studera X, Lawson JL, Chessel A, Geymonat M, Bortfeld-Miller M, Walter T, Wagstaff L, Piddini E, Carazo-Salas RE. Imaging Method: spinning disk confocal microscopy
In [7]:
plates = 0
images = 0
for plate in idr0001.listChildren():
plates += 1
for well in plate.listChildren():
images += len(list(well.listChildren()))
print("Plates:", plates)
print("Images:", images)
Plates: 192 Images: 109728
In [8]:
total = None
for plate in idr0001.listChildren():
grid = plate.getWellGrid()
single = np.zeros((len(grid), len(grid[0])))
if total is None:
total = np.zeros((len(grid), len(grid[0])))
for x, row in enumerate(grid):
for y, col in enumerate(row):
single[x][y] = grid[x][y].getImage().getROICount()
total += single
break # Continue to tally all ROIs
Disconnect when done loading data¶
In [13]:
conn.close()
Display results¶
In [14]:
plt.title('ROIs per well of %s' % plate.id)
plt.pcolor(total)
plt.colorbar()
plt.show()
License¶
Copyright (C) 2016-2019 University of Dundee. All Rights Reserved. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.