same Example_FLIM.lif has 32 bit images in it that aicsimageio cannot read

[ronnkling]

It handles the 8 and 16 bit OK
(base) PS E:\users\klingr\IDL_nih\readlif-0.6.5\readlif\testingLIFreader> conda activate py310
(py310) PS E:\users\klingr\IDL_nih\readlif-0.6.5\readlif\testingLIFreader> python
Python 3.10.11 | packaged by Anaconda, Inc. | (main, Apr 20 2023, 18:56:50) [MSC v.1916 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.

lazy_t0 = img.get_image_dask_data("CZYX", T=0) # returns out-of-memory 4D dask array
Traceback (most recent call last):
File "", line 1, in
NameError: name 'img' is not defined
lazy_t0 = img.get_image_dask_data("CZYX", T=0) # returns out-of-memory 4D dask array
Traceback (most recent call last):
File "", line 1, in
NameError: name 'img' is not defined
from aicsimageio import AICSImage
img = AICSImage('Example_FLIM.lif')
File "", line 1
img = AICSImage('Example_FLIM.lif')
IndentationError: unexpected indent
img = AICSImage('Example_FLIM.lif')
img.scenes
('M1 F1', 'M1 F1/FLIM/Intensity', 'M1 F1/FLIM/Fast Flim', 'M1 F1/FLIM/Standard Deviation', 'M1 F1/FLIM/Pattern Matching Scatter Plot Channel 1', 'M1 F1/FLIM/Phasor Real', 'M1 F1/FLIM/Phasor Imaginary', 'M1 F1/FLIM/Phasor Intensity', 'M1 F1/FLIM/Phasor Real Filtered', 'M1 F1/FLIM/Phasor Imaginary Filtered', 'M1 F1/FLIM/Phasor Mask', 'M1 F1/FLIM/Phasor Plot', 'M1 F2', 'M1 F2/FLIM/Intensity', 'M1 F2/FLIM/Fast Flim', 'M1 F2/FLIM/Standard Deviation', 'M1 F2/FLIM/Pattern Matching Scatter Plot Channel 1', 'M1 F2/FLIM/Phasor Real', 'M1 F2/FLIM/Phasor Imaginary', 'M1 F2/FLIM/Phasor Intensity', 'M1 F2/FLIM/Phasor Real Filtered', 'M1 F2/FLIM/Phasor Imaginary Filtered', 'M1 F2/FLIM/Phasor Mask', 'M1 F2/FLIM/Phasor Plot', 'M1 F3 -- fiber moved', 'M1 F3 -- fiber moved/FLIM/Intensity', 'M1 F3 -- fiber moved/FLIM/Fast Flim', 'M1 F3 -- fiber moved/FLIM/Standard Deviation', 'M1 F3 -- fiber moved/FLIM/Pattern Matching Scatter Plot Channel 1', 'M1 F4-5', 'M1 F4-5/FLIM/Intensity', 'M1 F4-5/FLIM/Fast Flim', 'M1 F4-5/FLIM/Standard Deviation', 'M1 F4-5/FLIM/Pattern Matching Scatter Plot Channel 1', 'Series005', 'Series005/FLIM/Intensity', 'Series005/FLIM/Fast Flim', 'Series005/FLIM/Standard Deviation', 'Series005/FLIM/Pattern Matching Scatter Plot Channel 1', 'M1 F6', 'M1 F6/FLIM/Intensity', 'M1 F6/FLIM/Fast Flim', 'M1 F6/FLIM/Standard Deviation', 'M1 F6/FLIM/Pattern Matching Scatter Plot Channel 1', 'M1 F7-8-9', 'M1 F7-8-9/FLIM/Intensity', 'M1 F7-8-9/FLIM/Fast Flim', 'M1 F7-8-9/FLIM/Standard Deviation', 'M1 F7-8-9/FLIM/Pattern Matching Scatter Plot Channel 1', 'M2 F1-2-3', 'M2 F1-2-3/FLIM/Intensity', 'M2 F1-2-3/FLIM/Fast Flim', 'M2 F1-2-3/FLIM/Standard Deviation', 'M2 F1-2-3/FLIM/Pattern Matching Scatter Plot Channel 1', 'M2 F4-5', 'M2 F4-5/FLIM/Intensity', 'M2 F4-5/FLIM/Fast Flim', 'M2 F4-5/FLIM/Standard Deviation', 'M2 F4-5/FLIM/Pattern Matching Scatter Plot Channel 1', 'M2 F6-7', 'M2 F6-7/FLIM/Intensity', 'M2 F6-7/FLIM/Fast Flim', 'M2 F6-7/FLIM/Standard Deviation', 'M2 F6-7/FLIM/Pattern Matching Scatter Plot Channel 1', 'M2 F8', 'M2 F8/FLIM/Intensity', 'M2 F8/FLIM/Fast Flim', 'M2 F8/FLIM/Standard Deviation', 'M2 F8/FLIM/Pattern Matching Scatter Plot Channel 1', 'M2 F8/FLIM/Phasor Real', 'M2 F8/FLIM/Phasor Imaginary', 'M2 F8/FLIM/Phasor Intensity', 'M2 F8/FLIM/Phasor Real Filtered', 'M2 F8/FLIM/Phasor Imaginary Filtered', 'M2 F8/FLIM/Phasor Mask', 'M2 F8/FLIM/Phasor Plot', 'M2 F8/FLIM/Phasor Plot Region 1', 'M2 F9', 'M2 F9/FLIM/Intensity', 'M2 F9/FLIM/Fast Flim', 'M2 F9/FLIM/Standard Deviation', 'M2 F9/FLIM/Pattern Matching Scatter Plot Channel 1', 'M2 F9/FLIM/Phasor Real', 'M2 F9/FLIM/Phasor Imaginary', 'M2 F9/FLIM/Phasor Intensity', 'M2 F9/FLIM/Phasor Real Filtered', 'M2 F9/FLIM/Phasor Imaginary Filtered', 'M2 F9/FLIM/Phasor Mask', 'M2 F9/FLIM/Phasor Plot', 'M2 F10', 'M2 F10/FLIM/Intensity', 'M2 F10/FLIM/Fast Flim', 'M2 F10/FLIM/Standard Deviation', 'M2 F10/FLIM/Pattern Matching Scatter Plot Channel 1')
img.set_scene(1)
img.current_scene
'M1 F1/FLIM/Intensity'
img.data
Traceback (most recent call last):
File "", line 1, in
File "C:\Users\klingr\anaconda3\envs\py310\lib\site-packages\aicsimageio\aics_image.py", line 542, in data
return self.xarray_data.data
File "C:\Users\klingr\anaconda3\envs\py310\lib\site-packages\aicsimageio\aics_image.py", line 482, in xarray_data
and dimensions.DimensionNames.MosaicTile in self.reader.dims.order
File "C:\Users\klingr\anaconda3\envs\py310\lib\site-packages\aicsimageio\readers\reader.py", line 532, in dims
self._dims = Dimensions(dims=self.xarray_dask_data.dims, shape=self.shape)
File "C:\Users\klingr\anaconda3\envs\py310\lib\site-packages\aicsimageio\readers\reader.py", line 359, in xarray_dask_data
self._xarray_dask_data = self._read_delayed()
File "C:\Users\klingr\anaconda3\envs\py310\lib\site-packages\aicsimageio\readers\lif_reader.py", line 484, in _read_delayed
image_data = self._create_dask_array(lif, dims)
File "C:\Users\klingr\anaconda3\envs\py310\lib\site-packages\aicsimageio\readers\lif_reader.py", line 317, in _create_dask_array
sample_plane = np.asarray(selected_scene.get_frame())
File "C:\Users\klingr\anaconda3\envs\py310\lib\site-packages\readlif\reader.py", line 380, in get_frame
return self._get_item(item_requested)
File "C:\Users\klingr\anaconda3\envs\py310\lib\site-packages\readlif\reader.py", line 182, in _get_item
raise ValueError("Unknown bit-depth, please submit a bug report"
ValueError: Unknown bit-depth, please submit a bug report on Github

[ronnkling]

is there a plan as to when this will be fixed?

[SeanLeRoy]

I believe the issue you created in the readlif repository is the main path forward, however since it seems that package hasn't been developed on in 2 years it is unknown when/if it will be fixed. Our other options are to use another python LIF reader, perhaps this one (or any you might know of), but I'm unsure if it necessarily be any better than readlif.

[SeanLeRoy]

Moving this issue over to bioio-lif. aicsimageio is moving into "maintenance" mode where only easy to implement bugfixes deemed critical (or community contributed) work will be done in aicsimageio. Instead of aicsimageio, we are creating a package soon to be released called bioio and plugins like the one aforementioned. See the reason for this change here.