Napari Visualization tool for Trackmate > 6.0 and bTrackmate XML files for 2/3D + time tracks. Available via pip package napatrackmater.
Home Page: https://pypi.org/project/napatrackmater/
License: BSD 3-Clause "New" or "Revised" License
![dependabot[bot] avatar](https://avatars.githubusercontent.com/in/29110?v=4 "dependabot[bot]")
I tired to use your plugin to visualize existing tracks generated using TrackMate, but encounter an erro once I pressed the compute button:
axes is TZYX
(42, 36, 1024, 1024)
(42, 36, 1024, 1024)
INFO: GPU available: False, used: False
15:34:57 INFO GPU available: False, used: False
INFO: TPU available: False, using: 0 TPU cores
15:34:57 INFO TPU available: False, using: 0 TPU cores
INFO: IPU available: False, using: 0 IPUs
15:34:57 INFO IPU available: False, using: 0 IPUs
INFO: HPU available: False, using: 0 HPUs
15:34:57 INFO HPU available: False, using: 0 HPUs
---------------------------------------------------------------------------
PermissionError Traceback (most recent call last)
File src\psygnal\_signal.py:990, in _run_emit_loop()
File src\psygnal\_weak_callback.py:321, in cb()
File D:\CONDA_ENV\napatrackmater-aiscimageio-napari\lib\site-packages\vollseg_na
pari_trackmate\_widget.py:135, in plugin_wrapper_track.<locals>.change_handler.<
locals>.decorator_change_handler.<locals>.wrapper(*args=())
134 print(f"{str(emitter.name).upper()}: {source.name}")
--> 135 return handler(*args)
handler = <function plugin_wrapper_track.<locals>._compute at 0x00000069
239A8F70>
args = ()
File D:\CONDA_ENV\napatrackmater-aiscimageio-napari\lib\site-packages\vollseg_na
pari_trackmate\_widget.py:2011, in plugin_wrapper_track.<locals>._compute()
2008 @change_handler(plugin_data.compute_button)
2009 def _compute():
-> 2011 _actual_computer()
File D:\CONDA_ENV\napatrackmater-aiscimageio-napari\lib\site-packages\vollseg_na
pari_trackmate\_widget.py:2083, in plugin_wrapper_track.<locals>._actual_compute
r()
2081 accelerator = "cpu"
-> 2083 _trackmate_objects = TrackMate(
_trackmate_objects = None
plugin_data = <FunctionGui plugin_data(image: napari.layers.image.image.
Image = <Image layer 'KO2_ATG5LECKO_231123_c3_cropped.ome' at 0x691cfb3940>, seg
_image: napari.layers.labels.labels.Labels = <Labels layer 'KO2_ATG5LECKO_231123
_cell_labels_cropped.ome' at 0x6920894730>, channel_seg_image: napari.layers.lab
els.labels.Labels = None, mask_image: napari.layers.labels.labels.Labels = None,
xml_path=WindowsPath('E:/Benjamin/Diede/test/KO2_ATG5LECKO_231123_cell_labels_c
ropped.ome.xml'), master_xml_path=WindowsPath('.'), track_csv_path=WindowsPath('
E:/Benjamin/Diede/test/tracks.csv'), spot_csv_path=WindowsPath('E:/Benjamin/Died
e/test/spots.csv'), edges_csv_path=WindowsPath('.'), cluster_csv_path=WindowsPat
h('.'), axes='TZYX', batch_size=8, device_type='cpu', compute_button=False) -> L
ist[LayerDataTuple]>
AttributeBoxname = 'AttributeIDBox'
TrackAttributeBoxname = 'TrackAttributeIDBox'
TrackidBox = 'All'
x_channel_seg = None
x_seg = <class 'numpy.ndarray'> (42, 36, 1024, 1024) uint16
x = <class 'numpy.ndarray'> (42, 36, 1024, 1024) uint16
x_mask = None
autoencoder_model = None
num_points = 0
plugin = <FunctionGui plugin(viewer: napari.viewer.Viewer = Viewer(camer
a=Camera(center=(0.0, 511.5, 511.5), zoom=0.11617840495573231, angles=(0.0, 0.0,
90.0), perspective=0.0, mouse_pan=True, mouse_zoom=True), cursor=Cursor(positio
n=(20.0, 17.0, -1067.9672703528113, 1006.4284454212805), scaled=True, size=10, s
tyle=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=4, ndisplay=2, last_use
d=0, range=((0.0, 42.0, 1.0), (0.0, 36.0, 1.0), (0.0, 1024.0, 1.0), (0.0, 1024.0
, 1.0)), current_step=(20, 17, 511, 511), order=(0, 1, 2, 3), axis_labels=('0',
'1', '2', '3')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layer
s=[<Image layer 'KO2_ATG5LECKO_231123_c3_cropped.ome' at 0x691cfb3940>, <Labels
layer 'KO2_ATG5LECKO_231123_cell_labels_cropped.ome' at 0x6920894730>], help='',
status='', tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari
', mouse_over_canvas=False, mouse_move_callbacks=[], mouse_drag_callbacks=[], mo
use_double_click_callbacks=[<function plugin_wrapper_track.<locals>.get_event at
0x000000691CCDA160>, <function plugin_wrapper_track.<locals>.get_event at 0x000
0006925C6FE50>], mouse_wheel_callbacks=[<function dims_scroll at 0x000000697B235
550>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keyma
p={}), label_head='<br>Citation <tt><a href="https://doi.org/10.25080/majora-1b6
fd038-014" style="color:gray;">NapaTrackMater Scipy</a></tt>', track_model_type=
'Non-Dividing', track_id_box=None, track_id_value='', cloud_auto_encoder_model_t
ype='No(Encoder)', cloud_auto_encoder_model='xenopus_nuclei_autoencoder', cloud_
auto_encoder_model_none='', model_folder_cloud_auto=WindowsPath('C:/Users/bpavie
'), progress_bar: magicgui.widgets.ProgressBar = ProgressBar(value=<function mat
ch_type.<locals>.<lambda> at 0x0000006925FB28B0>, annotation=<class 'magicgui.wi
dgets.ProgressBar'>, name='progress_bar')) -> List[LayerDataTuple]>
accelerator = 'cpu'
scale_z = 1
scale_xy = 1
2084 plugin_data.xml_path.value,
2085 plugin_data.spot_csv_path.value,
2086 plugin_data.track_csv_path.value,
2087 plugin_data.edges_csv_path.value,
2088 AttributeBoxname,
2089 TrackAttributeBoxname,
2090 TrackidBox,
2091 plugin_data.axes.value,
2092 master_xml_path=plugin_data.master_xml_path.value,
2093 channel_seg_image=x_channel_seg,
2094 seg_image=x_seg,
2095 image=x,
2096 mask=x_mask,
2097 autoencoder_model=autoencoder_model,
2098 num_points=num_points,
2099 progress_bar=plugin.progress_bar,
2100 batch_size=plugin_data.batch_size.value,
2101 accelerator=accelerator,
2102 devices=1,
2103 scale_z=scale_z,
2104 scale_xy=scale_xy,
2105 )
2106 nonlocal track_centroid_tree, track_centroid_list
File D:\CONDA_ENV\napatrackmater-aiscimageio-napari\lib\site-packages\napatrackm
ater\Trackmate.py:90, in TrackMate.__init__(self=<napatrackmater.Trackmate.Track
Mate object>, xml_path=WindowsPath('E:/Benjamin/Diede/test/KO2_ATG5LECKO_231123_
cell_labels_cropped.ome.xml'), spot_csv_path=WindowsPath('E:/Benjamin/Diede/test
/spots.csv'), track_csv_path=WindowsPath('E:/Benjamin/Diede/test/tracks.csv'), e
dges_csv_path=WindowsPath('.'), AttributeBoxname='AttributeIDBox', TrackAttribut
eBoxname='TrackAttributeIDBox', TrackidBox='All', axes='TZYX', scale_z=1, scale_
xy=1, latent_features=1, center=True, progress_bar=ProgressBar(value=<function m
atch_type.<locals>....icgui.widgets.ProgressBar'>, name='progress_bar'), acceler
ator='cpu', devices=1, master_xml_path=WindowsPath('.'), master_extra_name='', s
eg_image=<class 'numpy.ndarray'> (42, 36, 1024, 1024) uint16, channel_seg_image=
None, image=<class 'numpy.ndarray'> (42, 36, 1024, 1024) uint16, mask=None, four
ier=True, autoencoder_model=None, num_points=0, batch_size=8, compute_with_autoe
ncoder=True)
89 self.track_dataset, self.track_dataset_index = get_csv_data(self.track_c
sv_path)
---> 90 self.edges_dataset, self.edges_dataset_index = get_csv_data(self.edges_c
sv_path)
self.edges_csv_path = WindowsPath('.')
self = <napatrackmater.Trackmate.TrackMate object at 0x000000692193FEB0>
91 self.progress_bar = progress_bar
File D:\CONDA_ENV\napatrackmater-aiscimageio-napari\lib\site-packages\napatrackm
ater\Trackmate.py:2726, in get_csv_data(csv=WindowsPath('.'))
2724 def get_csv_data(csv):
-> 2726 dataset = pd.read_csv(
pd = <module 'pandas' from 'D:\\CONDA_ENV\\napatrackmater-aiscimageio-na
pari\\lib\\site-packages\\pandas\\__init__.py'>
csv = WindowsPath('.')
2727 csv, delimiter=",", encoding="unicode_escape", low_memory=False
2728 )[3:]
2729 dataset_index = dataset.index
File D:\CONDA_ENV\napatrackmater-aiscimageio-napari\lib\site-packages\pandas\io\
parsers\readers.py:912, in read_csv(filepath_or_buffer=WindowsPath('.'), sep=<no
_default>, delimiter=',', header='infer', names=<no_default>, index_col=None, us
ecols=None, dtype=None, engine=None, converters=None, true_values=None, false_va
lues=None, skipinitialspace=False, skiprows=None, skipfooter=0, nrows=None, na_v
alues=None, keep_default_na=True, na_filter=True, verbose=False, skip_blank_line
s=True, parse_dates=None, infer_datetime_format=<no_default>, keep_date_col=Fals
e, date_parser=<no_default>, date_format=None, dayfirst=False, cache_dates=True,
iterator=False, chunksize=None, compression='infer', thousands=None, decimal='.
', lineterminator=None, quotechar='"', quoting=0, doublequote=True, escapechar=N
one, comment=None, encoding='unicode_escape', encoding_errors='strict', dialect=
None, on_bad_lines='error', delim_whitespace=False, low_memory=False, memory_map
=False, float_precision=None, storage_options=None, dtype_backend=<no_default>)
910 kwds.update(kwds_defaults)
--> 912 return _read(filepath_or_buffer, kwds)
kwds = {'delimiter': ',', 'header': 'infer', 'names': None, 'index_col':
None, 'usecols': None, 'dtype': None, 'engine': 'c', 'converters': None, 'true_
values': None, 'false_values': None, 'skipinitialspace': False, 'skiprows': None
, 'skipfooter': 0, 'nrows': None, 'na_values': None, 'keep_default_na': True, 'n
a_filter': True, 'verbose': False, 'skip_blank_lines': True, 'parse_dates': Fals
e, 'infer_datetime_format': <no_default>, 'keep_date_col': False, 'date_parser':
<no_default>, 'date_format': None, 'dayfirst': False, 'cache_dates': True, 'ite
rator': False, 'chunksize': None, 'compression': 'infer', 'thousands': None, 'de
cimal': '.', 'lineterminator': None, 'quotechar': '"', 'quoting': 0, 'doublequot
e': True, 'escapechar': None, 'comment': None, 'encoding': 'unicode_escape', 'en
coding_errors': 'strict', 'dialect': None, 'on_bad_lines': <BadLineHandleMethod.
ERROR: 0>, 'delim_whitespace': False, 'low_memory': False, 'memory_map': False,
'float_precision': None, 'storage_options': None, 'dtype_backend': <no_default>,
'engine_specified': False}
filepath_or_buffer = WindowsPath('.')
File D:\CONDA_ENV\napatrackmater-aiscimageio-napari\lib\site-packages\pandas\io\
parsers\readers.py:577, in _read(filepath_or_buffer=WindowsPath('.'), kwds={'cac
he_dates': True, 'chunksize': None, 'comment': None, 'compression': 'infer', 'co
nverters': None, 'date_format': None, 'date_parser': <no_default>, 'dayfirst': F
alse, 'decimal': '.', 'delim_whitespace': False, ...})
576 # Create the parser.
--> 577 parser = TextFileReader(filepath_or_buffer, **kwds)
TextFileReader = <class 'pandas.io.parsers.readers.TextFileReader'>
filepath_or_buffer = WindowsPath('.')
kwds = {'delimiter': ',', 'header': 'infer', 'names': None, 'index_col':
None, 'usecols': None, 'dtype': None, 'engine': 'c', 'converters': None, 'true_
values': None, 'false_values': None, 'skipinitialspace': False, 'skiprows': None
, 'skipfooter': 0, 'nrows': None, 'na_values': None, 'keep_default_na': True, 'n
a_filter': True, 'verbose': False, 'skip_blank_lines': True, 'parse_dates': Fals
e, 'infer_datetime_format': <no_default>, 'keep_date_col': False, 'date_parser':
<no_default>, 'date_format': None, 'dayfirst': False, 'cache_dates': True, 'ite
rator': False, 'chunksize': None, 'compression': 'infer', 'thousands': None, 'de
cimal': '.', 'lineterminator': None, 'quotechar': '"', 'quoting': 0, 'doublequot
e': True, 'escapechar': None, 'comment': None, 'encoding': 'unicode_escape', 'en
coding_errors': 'strict', 'dialect': None, 'on_bad_lines': <BadLineHandleMethod.
ERROR: 0>, 'delim_whitespace': False, 'low_memory': False, 'memory_map': False,
'float_precision': None, 'storage_options': None, 'dtype_backend': <no_default>,
'engine_specified': False}
579 if chunksize or iterator:
File D:\CONDA_ENV\napatrackmater-aiscimageio-napari\lib\site-packages\pandas\io\
parsers\readers.py:1407, in TextFileReader.__init__(self=<pandas.io.parsers.read
ers.TextFileReader object>, f=WindowsPath('.'), engine='c', **kwds={'cache_dates
': True, 'chunksize': None, 'comment': None, 'compression': 'infer', 'converters
': None, 'date_format': None, 'date_parser': <no_default>, 'dayfirst': False, 'd
ecimal': '.', 'delim_whitespace': False, ...})
1406 self.handles: IOHandles | None = None
-> 1407 self._engine = self._make_engine(f, self.engine)
self.engine = 'c'
self = <pandas.io.parsers.readers.TextFileReader object at 0x0000006926C
7E250>
f = WindowsPath('.')
File D:\CONDA_ENV\napatrackmater-aiscimageio-napari\lib\site-packages\pandas\io\
parsers\readers.py:1661, in TextFileReader._make_engine(self=<pandas.io.parsers.
readers.TextFileReader object>, f=WindowsPath('.'), engine='c')
1660 mode += "b"
-> 1661 self.handles = get_handle(
self.handles = None
self = <pandas.io.parsers.readers.TextFileReader object at 0x0000006926C
7E250>
f = WindowsPath('.')
mode = 'r'
self.options = {'delimiter': ',', 'escapechar': None, 'quotechar': '"',
'quoting': 0, 'doublequote': True, 'skipinitialspace': False, 'lineterminator':
None, 'header': 0, 'index_col': None, 'names': None, 'skiprows': set(), 'na_valu
es': {'', '#N/A', '-NaN', '-1.#QNAN', 'null', '-1.#IND', 'NULL', 'n/a', '-nan',
'N/A', 'NaN', '1.#QNAN', '1.#IND', 'None', '#NA', 'nan', 'NA', '#N/A N/A', '<NA>
'}, 'keep_default_na': True, 'true_values': None, 'false_values': None, 'convert
ers': {}, 'dtype': None, 'cache_dates': True, 'thousands': None, 'comment': None
, 'decimal': '.', 'parse_dates': False, 'keep_date_col': False, 'dayfirst': Fals
e, 'date_parser': <no_default>, 'date_format': None, 'usecols': None, 'verbose':
False, 'encoding': 'unicode_escape', 'compression': 'infer', 'skip_blank_lines'
: True, 'encoding_errors': 'strict', 'on_bad_lines': <BadLineHandleMethod.ERROR:
0>, 'dtype_backend': <no_default>, 'delim_whitespace': False, 'na_filter': True
, 'low_memory': False, 'memory_map': False, 'float_precision': None, 'storage_op
tions': None, 'na_fvalues': set()}
is_text = True
1662 f,
1663 mode,
1664 encoding=self.options.get("encoding", None),
1665 compression=self.options.get("compression", None),
1666 memory_map=self.options.get("memory_map", False),
1667 is_text=is_text,
1668 errors=self.options.get("encoding_errors", "strict"),
1669 storage_options=self.options.get("storage_options", None),
1670 )
1671 assert self.handles is not None
File D:\CONDA_ENV\napatrackmater-aiscimageio-napari\lib\site-packages\pandas\io\
common.py:859, in get_handle(path_or_buf=WindowsPath('.'), mode='r', encoding='u
nicode_escape', compression=None, memory_map=False, is_text=True, errors='strict
', storage_options=None)
857 if ioargs.encoding and "b" not in ioargs.mode:
858 # Encoding
--> 859 handle = open(
handle = '.'
ioargs = IOArgs(filepath_or_buffer='.', encoding='unicode_escape', mode=
'r', compression={'method': None}, should_close=False)
ioargs.mode = 'r'
ioargs.encoding = 'unicode_escape'
errors = 'strict'
860 handle,
861 ioargs.mode,
862 encoding=ioargs.encoding,
863 errors=errors,
864 newline="",
865 )
866 else:
867 # Binary mode
PermissionError: [Errno 13] Permission denied: '.'
The above exception was the direct cause of the following exception:
EmitLoopError Traceback (most recent call last)
File D:\CONDA_ENV\napatrackmater-aiscimageio-napari\lib\site-packages\magicgui\w
idgets\bases\_value_widget.py:71, in ValueWidget._on_value_change(self=PushButto
n(value=False, annotation=<class 'inspect._empty'>, name='compute_button'), valu
e=False)
69 if value is self.null_value and not self._nullable:
70 return
---> 71 self.changed.emit(value)
value = False
self.changed = <SignalInstance 'changed' on PushButton(value=False, anno
tation=<class 'inspect._empty'>, name='compute_button')>
self = PushButton(value=False, annotation=<class 'inspect._empty'>, name
='compute_button')
File src\psygnal\_signal.py:945, in emit()
File src\psygnal\_signal.py:992, in _run_emit_loop()
EmitLoopError:
While emitting signal 'magicgui.widgets.PushButton.changed', an error occurred i
n callback 'vollseg_napari_trackmate._widget.plugin_wrapper_track.<locals>._comp
ute'.
The args passed to the callback were: (False,)
This is not a bug in psygnal. See 'PermissionError' above for details.
Is there anything I should have done to avoid this error ?
Best,
Benjamin
tests badge in README file not displaying
Hi @kapoorlab ,
I saw your announcement in the image.sc forum, and the combination of napari + TrackMate sounds just perfect for my purposes. Thank you for sharing the code and providing a pip package!
For a quick test, I started with your example notebook and changed the path_xml and SegmentationImage paths according to my file locations and set RawImage as well as MaskImage to None.
When I now continue in the notebook, it correctly creates the "Tracklets", but once it starts to compute them for TrackID 0 the following error message appears:
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-23-8a4f94a8c1bd> in <module>
----> 1 RegionID, VolumeID, locationID, Tracks, ID, StartID = TM.ImportTrackmateXML(
2 path_xml,Seg,
3 image = Raw,
4 Mask = Mask,
5 XYcalibration = XYcalibration,
C:\ProgramData\Anaconda3\envs\napatrackmater\lib\site-packages\napatrackmater\Trackmate.py in ImportTrackmateXML(xml_path, Segimage, XYcalibration, Zcalibration, Tcalibration, image, Mask, mintracklength)
535
536 TwoDCoordinates = [(prop.centroid[1] , prop.centroid[2]) for prop in properties]
--> 537 TwoDtree = spatial.cKDTree(TwoDCoordinates)
538 TwoDLocation = (y ,x)
539 closestpoint = TwoDtree.query(TwoDLocation)
ckdtree.pyx in scipy.spatial.ckdtree.cKDTree.__init__()
ValueError: data must be 2 dimensions
In trackmate I used a series of 3D images. You can find the trackmate xml file as well the segmentation results at:
https://datashare.mpcdf.mpg.de/s/AtEPeYkTtdlnBOi
So I'm trying to run the BTrackMateVisualization notebook and I'm running into memory issue.
My computer has 16 Gb of RAM and 8 Gb of swap, and I run out of memory.
If I run a profiler, the steps where it reads the images already takes 10 Gb of memory. And we didn't even start any computation at this point.
Is it necessary to read Raw as float16?
I am not sure what could be a good solution here. Splitting the example image in half? On one hand it's good to provide a full working example, on the other hand if one needs 32 Gb of RAM to run it, it might be limitating.
Another solution would be to read only the frame of interest when needed, and not load the full file in memory, if that's at all possible. You know best the intricacies of the software, so let me know what you think would be possible to do.
If we look at import_TM_XML, we can see that it really only needs the shape of the image, not the full image, so maybe provide that as parameters to the function instead of the full image, this way the full image can be discarded once we have its shape and we can free up memory.
Hi guys,
I am trying to use NapaTrackmater, but when I import it, I get the following error:
File "C:\Users\Simon Andersen\AppData\Roaming\Python\Python39\site-packages\kapoorlabs_lightning\lightning_trainer.py", line 626, in ClusterLightningDistModel
def predict_step(self, batch, batch_idx) -> STEP_OUTPUT | None:
TypeError: unsupported operand type(s) for |: '_UnionGenericAlias' and 'NoneType'
Since you have also made the lightning package, I figure this is the place to ask for help.
Greetings from Denmark
Simon
Dear all,
I can install the napatrackmate plugin through napari successfully but when I start the plugin I get this error:
\miniconda3\envs\napari\lib\site-packages\vollseg_napari_trackmate\_widget.py in plugin_wrapper_track()
27 def plugin_wrapper_track():
28
---> 29 from cellshape_cloud import CloudAutoEncoder
global cellshape_cloud = undefined
global CloudAutoEncoder = undefined
30 from cellshape_cluster import DeepEmbeddedClustering
31 from napatrackmater import load_json
ModuleNotFoundError: No module named 'cellshape_cloud'
Even if i do pip install cellshape_clould, it throws other errors
Can you please help me?
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