Cell Lineage in the adult mouse corpus callosum

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cell-lineage-in-the-adult-mouse-corpus-callosum
cell-lineage-in-the-adult-mouse-corpus-callosum
cell-lineage-in-the-adult-mouse-corpus-callosum
cell-lineage-in-the-adult-mouse-corpus-callosum
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Summary

This notebook demonstrates how to recreate lineages published in the paper Live imaging of remyelination in the adult mouse corpus callosum and available at idr0113-bottes-opcclones .

The lineage is created from the metadata associated to the specified image.

LPC-induced focal demyelination and in vivo imaging of genetically targeted OPCs and their progeny to describe the cellular dynamics of OPC-mediated remyelination in the CC.

Longitudinal observation of OPCs and their progeny for up to two months reveals functional inter- and intraclonal heterogeneity and provides insights into the cell division capacity and the migration/differentiation dynamics of OPCs and their daughter cells in vivo.

The majority of the clones remained quiescent or divided only few times. Some OPCs were highly proliferative. Large clones showed longer times between consecutive divisions compared to low proliferating clones.

OPCs show distinct modes of cell division: from symmetric proliferative, to symmetric differentiating and also asymmetric cell division, where the OPC is self-renewed while the other daughter cell differentiates.

Only 16.46% of OPC-derived cells differentiated into mature, remyelinating oligodendrocytes, with OPCs born at early divisions showing a higher probability to survive and to terminally differentiate.

Cell death was associated with distinct cell division histories of different clones, with higher probability of death when generated at later divisions.

Migratory behaviour was restricted to progenitors. Successfully differentiating progenitors moved shorter distances per day compared to dying cells.

Code Snippets

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# Parameters:
imageId = 13425213
Jupyter Notebook From line 2 of raw/idr0113_lineage.ipynb 
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import graphviz
import math
import requests
import pandas as pd

from os.path import expanduser

from idr import connection
Jupyter Notebook Pandas requests graphviz IDR From line 7 of raw/idr0113_lineage.ipynb 
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conn = connection('idr.openmicroscopy.org')
Jupyter Notebook From line 18 of raw/idr0113_lineage.ipynb 
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times = {}

image = conn.getObject("Image", imageId)
pixels_id = image.getPrimaryPixels().getId()
query = "from PlaneInfo as Info where pixels.id='" + str(pixels_id) + "'"
infos = conn.getQueryService().findAllByQuery(query, None)
for i in infos:
    times.update({i.theT.getValue(): int(i.deltaT.getValue())})
Jupyter Notebook From line 22 of raw/idr0113_lineage.ipynb 
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INDEX_PAGE = "https://idr.openmicroscopy.org/webclient/?experimenter=-1"
ROI_URL = "https://idr.openmicroscopy.org/api/v0/m/images/{key}/rois/?limit=500"
TABLE_URL = "https://idr.openmicroscopy.org/webgateway/table/Image/{key}/query/?query=*"
Jupyter Notebook From line 33 of raw/idr0113_lineage.ipynb 
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# create http session
with requests.Session() as session:
    request = requests.Request('GET', INDEX_PAGE)
    prepped = session.prepare_request(request)
    response = session.send(prepped)
    if response.status_code != 200:
        response.raise_for_status()
Jupyter Notebook From line 39 of raw/idr0113_lineage.ipynb 
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qs = {'key': imageId}
url = ROI_URL.format(**qs)
json_data = session.get(url).json()

roi_time_map = {}
# parse the json
for d in json_data['data']:
    roi_id = d['@id']
    for s in d["shapes"]:
        roi_time_map.update({str(roi_id): times.get(int(s['TheT']))})
Jupyter Notebook JSON From line 49 of raw/idr0113_lineage.ipynb 
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url = TABLE_URL.format(**qs)
json_data = session.get(url).json()
Jupyter Notebook From line 62 of raw/idr0113_lineage.ipynb 
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df = pd.DataFrame(columns=json_data['data']['columns'])
for r in json_data['data']['rows']:
    df.loc[len(df)] = r
Jupyter Notebook From line 67 of raw/idr0113_lineage.ipynb 
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def is_valid(row):
    mother = row["Mother Roi"]
    sister = row["Sister Roi"]
    if mother == "" and sister == "":
        return False
    return True
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def find_mothers():
    ids = []
    for index, row in df.iterrows():
        mother = row["Mother Roi"]
        if mother == "":
            continue
        v = str(mother)
        if v not in ids:
            ids.append(v)
    return ids
Jupyter Notebook From line 86 of raw/idr0113_lineage.ipynb 
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f = graphviz.Digraph(comment='Lineage', format='pdf')
f.attr(rank='sink')
f.attr('node', shape='circle')
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# Set various parametes used in the graph
COLOR_OPC = "red"
COLOR_PM = "orange"
COLOR_M = "cyan"
COLOR_DEAD = "purple"
COLOR_UNCERTAIN = "black"
COLOR_EDGE = "black"
STYLE_CERTAIN = "solid"
STYLE_UNCERTAIN = "dotted"
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ids = []
# determine the mothers rois
mothers = find_mothers()
for index, row in df.iterrows():
    id = str(row["Roi"])
    if is_valid(row) is False and id not in mothers:
        continue
    type = str(row["Cell Type"])
    ids.append(id)
    dead = "no"
    dead_value = str(row["Cell Death"])
    uncertainty = str(row["Cell Uncertainty"])
    value = "Type: %s\nCertainty: %s\nDays After Induction: %s\nROI ID: %s" % (type, uncertainty, roi_time_map.get(id), id)
    color = COLOR_OPC
    width = "0.1"
    if type == "PM":
        color = COLOR_PM
    elif type == "M":
        color = COLOR_M
    if uncertainty == "uncertain":
        color = "%s:%s" % (COLOR_UNCERTAIN, color)
        width = "0.2"
    f.node(id, "", URL='https://idr.openmicroscopy.org/iviewer/?roi=%s' % id, style="radial", color=color, fixedsize='true', width=width, tooltip=value)
    # Create a node indicating that the cell is dead
    if dead_value != "":
        nv = "dead_%s" % id
        f.node(nv, "", style='filled', color=COLOR_DEAD, fixedsize='true', width='0.1')
Jupyter Notebook From line 117 of raw/idr0113_lineage.ipynb 
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edges = []
for index, row in df.iterrows():
    if is_valid(row) is False:
        continue
    id = str(row["Roi"])
    color = COLOR_EDGE
    lineage = row["Lineage Roi"]
    if lineage != "":
        f.edge(str(int(lineage)), id, label='', color=color, arrowhead="none")  
    value = row["Mother Roi"]
    if value != "" and lineage == "":
        certainty = row["Mother Uncertainty"]
        style = STYLE_CERTAIN
        if certainty != "certain":
            style = STYLE_UNCERTAIN
        f.edge(str(int(value)), id, label='', color=color, style=style, arrowhead="none")        
    dead_value = str(row["Cell Death"])
    if dead_value != "":
        nv = "dead_%s" % id
        f.edge(id, nv, label='', color=color, arrowhead="none", tooltip="Cell is dead")
Jupyter Notebook From line 147 of raw/idr0113_lineage.ipynb 
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with f.subgraph(name='legend') as c:
    c.attr('node', shape='plaintext', fontsize='8')
    c.node("key1", label='''<<table border="0" cellpadding="2" cellspacing="0" cellborder="0">
      <tr><td align="left" port="i1">certain</td></tr>
      <tr><td align="left" port="i2">uncertain</td></tr>
      </table>>''')
    c.node("key2", label='''<<table border="0" cellpadding="2" cellspacing="0" cellborder="0">
      <tr><td align="right" port="i1">&nbsp;</td></tr>
      <tr><td align="right" port="i2">&nbsp;</td></tr>
      </table>>''')
    c.edge("key1:i1", "key2:i1", label='', color=COLOR_EDGE, style=STYLE_CERTAIN, arrowhead="none")
    c.edge("key1:i2", "key2:i2", label='', color=COLOR_EDGE, style=STYLE_UNCERTAIN, arrowhead="none")
    c.node("OPC")
    c.node("PM")
    c.node("M")
    c.node("Cell Death")
    c.node("Uncertain Cell Type")
    c.attr('node', shape='circle', fontsize='6')
    c.node("opc1", "", style='filled', color=COLOR_OPC, fixedsize='true', width='0.1')
    c.node("pm1", "", style='filled', color=COLOR_PM, fixedsize='true', width='0.1')
    c.node("m1", "", style='filled', color=COLOR_M, fixedsize='true', width='0.1')
    c.node("death1", "", style='filled', color=COLOR_DEAD, fixedsize='true', width='0.1')
    c.node("type1", "", style='filled', color=COLOR_UNCERTAIN, fixedsize='true', width='0.1')
    c.edge("OPC", "opc1", label='', style="invis")
    c.edge("PM", "pm1", label='', style="invis")
    c.edge("M", "m1", label='', style="invis")
    c.edge("Cell Death", "death1", label='', style="invis")
    c.edge("Uncertain Cell Type", "type1", label='', style="invis")
Jupyter Notebook From line 170 of raw/idr0113_lineage.ipynb 
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home = expanduser("~")
f.view(home+"/lineage_%s" % imageId)
Jupyter Notebook From line 205 of raw/idr0113_lineage.ipynb
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/IDR/idr0113-bottes-opcclones
Name: cell-lineage-in-the-adult-mouse-corpus-callosum
Version: Version 1
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Copyright: Public Domain
License: BSD 2-Clause "Simplified" License
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