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1. #Cellprofiler unmix color install
2. #Cellprofiler unmix color update
3. #Cellprofiler unmix color upgrade
4. #Cellprofiler unmix color code
5. #Cellprofiler unmix color windows

#Cellprofiler unmix color update

* #3648 Update requirements files with new bioformats versions * #3648 Bump python-bioformats version ( #3653) Without this change, it is a syntax error in Python 3 * Explicit tuple required inside a comprehension in Python 3 ( #3651) * from cellprofiler.modules import images * Revert cellprofiler/modules/loadsingleimage.py * Remove from _future_ import with_statement and from. * Remove from _future_ import absolute_import * Cleanup xxx_todo_changeme and doubled coding lines

#Cellprofiler unmix color install

* setup.py: permit pip install on Python 3.6.3 * No absolute_imports in cellprofiler/modules/images.py * Reference default strings in preferences, where they're defined * Import wx in function where it's used, spelling correction None of the other boxsizers had another reference, so I'm hoping this is fine. * Remove undefined groupbox reference in pipeline controller * Reference cellprofiler.pipelines directly This used a C file that no longer exists: cbd1d45

#Cellprofiler unmix color windows

* Remove windows specific check for hidden files * sr_alloc_block requires no extra arguments (expecially undefined ones) * Remove ImagePlaneDetailsMetadata which no longer existsĪlso set undefined "module" reference to None. * Travis CI: Add flake8 to find syntax errors and undefined names * Add "c" and "cmap" as options for subplot_scatter ( #3637) * eliminated separate elifs for BROWSE_FILES and BROWSE_FOLDER * working now (removed unnecessary debug information) * added on_pathlist_browse_folder calls in two more places * adding changes to add Select Folder context menu Put the class variable at the start of the class (to make issues like Added spacing around all operators I found Settings from the current version do not need any update. * Only update variable names if pipeline comes from older version Like this it can be verified that channel numbers Such that they contained the channel number they should * Adds a test to load an old pipeline from v3Ī v3 pipeline was added where images were named Reflect the fact that it is now integer values. This adapts the documentation of `Add channel` to Which required a slight adaptation of some tests. The channel_choice widget is now an cps.Integer * Adapted tests to channel_choice type change Tedious, as selecting channel idx 20 would require The previous solution was elegantĪnd supported that many channels, but was in practice Thus it would be convient to easily extract single We are dealing routinely with 30+ channel images. * Adapts the channel_choice widget to cps.Integer * Make the requirements more python-canonical * Specify at least a minimum version of numpy * #3622 Address potentially incorrect equality checkĪ number of other equality checks for object_name_variable in this file check against value rather than the actual object. * Build should succeed even if unpinned fails

#Cellprofiler unmix color upgrade

I hope that all users know that they should - in no case beside some graphics experiments - use the option to select more than 3 stains.* Don't upgrade when installing test dependencies The error varies with the concentrations of the stains. When more than 3 stains are used for a deconvolution of a signal with 3 components the deconvolution result is no longer correct.

Here are some results from the script for different concentrations, deconvolved with 3stains and 5stains.ģ stain mixture | deconvolution with 3 stainsģ stain mixture | deconvolution with 5 stainsĭeconvolution works perfect with 3 stains. MixtureSum = mixtureSum + stains,chn] * concCreate # CREATION OF LINEAR (!!!) STAIN MIXTURE # # (stainsCreate.size must be equal concCreate.size) If you deactivate line 51 in the script and activate line 52 instead you can see what happens if more than 3 stains are selected for deconvolution.Ĭompare the result concentration with the specified input concentrations. In the new version you can specify stains and their concentration for the creation of a stain mixture and the stains for the deconvolution. Print('inverted absorbance column: ' + str(n)) #of absorbances corresponding to the entered row. #returns a 3-tuple which is the column of the inverse of the matrix Result = result / np.sqrt(np.sum(result ** 2))ĭ_array = np.array()

#Cellprofiler unmix color code

(compare this test code to the original code) import numpy as np With the following reduce test code you can see how CellProfiler creates the stain vector matrix, invert it and separate single columns to apply them to the image This is the reason why CellProfiler can calculate with more then 3 stains.īut even if this calculation is technically possible it make physically no sense.