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2c_fibertyping.py 100755 → 100644
View file @ 8ad0e271
# this is a python rewrite of the original ijm published at
# this is a python rewrite of the original ijm published at
# https://github.com/Hyojung-Choo/Myosoft/blob/Myosoft-hub/Scripts/central%20nuclei%20counter.ijm
# IJ imports
......@@ -33,37 +33,47 @@ import os
def fix_ij_options():
"""put IJ into a defined state
"""Configure ImageJ (IJ) to a predefined state.
This function sets various options in ImageJ to ensure a consistent
environment for image processing tasks. It includes settings for appearance,
color management, binary image options, and file output format.
"""
# disable inverting LUT
# Disable inverting LUT (Look-Up Table) for images
IJ.run("Appearance...", " menu=0 16-bit=Automatic")
# set foreground color to be white, background black
# Set foreground color to be white and background color to be black, with red for selections
IJ.run("Colors...", "foreground=white background=black selection=red")
# black BG for binary images and pad edges when eroding
# Enable black background for binary images and pad edges when eroding
IJ.run("Options...", "black pad")
# set saving format to .txt files
# Set saving format to .txt files, saving both columns and rows
IJ.run("Input/Output...", "file=.txt save_column save_row")
# ============= DON’T MOVE UPWARDS =============
# set "Black Background" in "Binary Options"
# Set "Black Background" option for binary operations
IJ.run("Options...", "black")
# scale when converting = checked
# Enable scaling when converting images between types
IJ.run("Conversions...", "scale")
def fix_ij_dirs(path):
"""use forward slashes in directory paths
"""Replace backslashes with forward slashes in directory paths.
This function takes a directory path obtained from a dialogue or script
parameter and returns a more robust path with forward slashes as separators.
Parameters
----------
path : string
a directory path obtained from dialogue or script parameter
path : str
A directory path
Returns
-------
string
a more robust path with forward slashes as separators
str
A directory path with forward slashes as separators
"""
fixed_path = str(path).replace("\\", "/")
# fixed_path = fixed_path + "/"
......@@ -71,169 +81,239 @@ def fix_ij_dirs(path):
def open_image_with_BF(path_to_file):
""" use Bio-Formats to opens the first image from an image file path
"""Open the first image from a file using Bio-Formats.
This function utilizes Bio-Formats to open an image file and returns
the first image contained within the file. The image is opened in
grayscale mode with autoscaling enabled.
Parameters
----------
path_to_file : string
path to the image file
path_to_file : str
The file path to the image file to be opened.
Returns
-------
ImagePlus
the first imp stored in a give file
The first image contained in the specified file.
"""
# Create an ImporterOptions object for configuring the import process
options = ImporterOptions()
options.setColorMode(ImporterOptions.COLOR_MODE_GRAYSCALE)
# Set the color mode to grayscale
options.setColorMode(ImporterOptions.COLOR_MODE_COMPOSITE )
# Enable autoscaling for the image
options.setAutoscale(True)
# Set the file path for the image to be opened
options.setId(path_to_file)
imps = BF.openImagePlus(options) # is an array of ImagePlus
# Open the image(s) using Bio-Formats and store them in an array
imps = BF.openImagePlus(options)
# Return the first image in the array
return imps[0]
def fix_BF_czi_imagetitle(imp):
image_title = os.path.basename( imp.getShortTitle() )
"""
Fix the title of an image read using the bio-formats importer.
The title is modified to remove the ".czi" extension and replace
spaces with underscores.
Parameters
----------
imp : ij.ImagePlus
The image to be processed.
Returns
-------
str
The modified title of the image.
"""
# Get the short title of the image (without path)
image_title = os.path.basename(imp.getShortTitle())
# Remove the ".czi" extension
image_title = image_title.replace(".czi", "")
# Replace spaces with underscores
image_title = image_title.replace(" ", "_")
# Remove any double underscores
image_title = image_title.replace("_-_", "")
# Remove any double underscores
image_title = image_title.replace("__", "_")
# Remove any "#" characters
image_title = image_title.replace("#", "Series")
return image_title
def clear_ij_roi_manager(rm):
"""delete all ROIs from the RoiManager
"""
Clear all ROIs from the RoiManager.
Parameters
----------
rm : RoiManager
rm : ij.plugin.frame.RoiManager
a reference of the IJ-RoiManager
"""
# Run the "reset" command in the RoiManager to clear all ROIs
rm.runCommand('reset')
def get_threshold_from_method(imp, channel, method):
"""returns the threshold value of chosen IJ AutoThreshold method in desired channel
"""Get the threshold value of chosen IJ AutoThreshold method in desired channel.
Parameters
----------
imp : ImagePlus
the imp from which to get the threshold value
channel : integer
the channel in which to get the treshold
method : string
the AutoThreshold method to use
The imp from which to get the threshold value.
channel : int
The channel in which to get the threshold.
method : str
The AutoThreshold method to use.
Returns
-------
list
the upper and the lower threshold (integer values)
A list containing the upper and the lower threshold (integer values).
"""
# Set the channel of the imp to the desired channel
imp.setC(channel) # starts at 1
# Get the processor of the imp
ip = imp.getProcessor()
# Set the AutoThreshold method to the desired method
ip.setAutoThreshold(method + " dark")
# Get the minimum and maximum threshold values
lower_thr = ip.getMinThreshold()
upper_thr = ip.getMaxThreshold()
# Reset the threshold so that the imp is not affected by this function
ip.resetThreshold()
return lower_thr, upper_thr
return [lower_thr, upper_thr]
def measure_in_all_rois( imp, channel, rm ):
"""measures in all ROIS on a given channel of imp all parameters that are set in IJ "Set Measurements"
"""Measures in all ROIs on a given channel of imp all parameters that are set in IJ "Set Measurements".
This function takes an ImagePlus (imp), a channel (integer, starts at 1), and a RoiManager (rm) as
parameters. It then sets the channel of the imp to the desired channel, deselects all ROIs in the
RoiManager, and measures in all ROIs of the RoiManager on the channel of the imp. The parameters
that are measured are the ones that are set in IJ "Set Measurements".
Parameters
----------
imp : ImagePlus
imp : ij.ImagePlus
the imp to measure on
channel : integer
channel : int
the channel to measure in. starts at 1.
rm : RoiManager
rm : ij.plugin.frame.RoiManager
a reference of the IJ-RoiManager
"""
# Set the channel of the imp to the desired channel
imp.setC(channel)
# Deselect all ROIs in the RoiManager
rm.runCommand(imp,"Deselect")
# Measure in all ROIs of the RoiManager on the channel of the imp
rm.runCommand(imp,"Measure")
def change_all_roi_color( rm, color ):
"""change the color of all ROIs in the RoiManager
def change_all_roi_color(rm, color):
"""
Change the color of all ROIs in the RoiManager.
Parameters
----------
rm : RoiManager
a reference of the IJ-RoiManager
color : string
the desired color. e.g. "green", "red", "yellow", "magenta" ...
rm : ij.plugin.frame.RoiManager
A reference to the IJ-RoiManager.
color : str
The desired color, e.g., "green", "red", "yellow", "magenta".
Returns
-------
None
"""
number_of_rois = rm.getCount()
for roi in range( number_of_rois ):
rm.select(roi)
rm.runCommand("Set Color", color)
# Select all ROIs in the RoiManager
#rm.setSelectedIndexes(range(rm.getCount()))
rm.runCommand("Deselect")
# Change the color of all ROIs to the desired color
rm.runCommand("Set Color", color)
# # Deselect all ROIs again to finalize changes
# rm.runCommand("Deselect")
def change_subset_roi_color( rm, selected_rois, color ):
"""change the color of selected ROIs in the RoiManager
def change_subset_roi_color(rm, selected_rois, color):
"""
Change the color of selected ROIs in the RoiManager.
Parameters
----------
rm : RoiManager
a reference of the IJ-RoiManager
selected_rois : array
ROIs in the RoiManager to change
color : string
the desired color. e.g. "green", "red", "yellow", "magenta" ...
rm : ij.plugin.frame.RoiManager
A reference to the IJ-RoiManager.
selected_rois : list of int
Indices of ROIs in the RoiManager to change.
color : str
The desired color, e.g., "green", "red", "yellow", "magenta", etc.
"""
# Deselect all currently selected ROIs in the RoiManager
rm.runCommand("Deselect")
# Select the specified ROIs by their indices
rm.setSelectedIndexes(selected_rois)
# Change the color of the selected ROIs to the specified color
rm.runCommand("Set Color", color)
# Deselect all ROIs again to finalize changes
rm.runCommand("Deselect")
def show_all_rois_on_image(rm, imp):
"""shows all ROIs in the ROiManager on imp
"""
Display all ROIs on the given image using the ROI Manager.
Parameters
----------
rm : RoiManager
a reference of the IJ-RoiManager
imp : ImagePlus
the imp on which to show the ROIs
rm : ij.plugin.frame.RoiManager
A reference to the IJ-RoiManager.
imp : ij.ImagePlus
The image on which to display the ROIs.
"""
# Show the image in the ImageJ window
imp.show()
rm.runCommand(imp,"Show All")
# Use the ROI Manager to show all ROIs on the image
rm.runCommand(imp, "Show All")
def save_all_rois(rm, target):
"""save all ROIs in the RoiManager as zip to target path
"""Save all ROIs in the RoiManager as a zip file to the given target path.
Parameters
----------
rm : RoiManager
a reference of the IJ-RoiManager
target : string
the path in to store the ROIs. e.g. /my-images/resulting_rois.zip
rm : ij.plugin.frame.RoiManager
A reference to the IJ-RoiManager.
target : str
The file path in which to save the ROIs, e.g., /my-images/resulting_rois.zip
"""
# Save all ROIs in the RoiManager to the given target path
rm.runCommand("Save", target)
def save_selected_rois( rm, selected_rois, target ):
"""save selected ROIs in the RoiManager as zip to target path
def save_selected_rois(rm, selected_rois, target):
"""
Save selected ROIs in the RoiManager as a zip file to the given target path.
Parameters
----------
rm : RoiManager
a reference of the IJ-RoiManager
selected_rois : array
ROIs in the RoiManager to save
target : string
the path in to store the ROIs. e.g. /my-images/resulting_rois_subset.zip
rm : ij.plugin.frame.RoiManager
A reference to the IJ-RoiManager.
selected_rois : list of int
Indices of ROIs in the RoiManager to save.
target : str
The file path in which to save the ROIs, e.g., /my-images/resulting_rois_subset.zip
"""
# Deselect all currently selected ROIs in the RoiManager to ensure a clean start
rm.runCommand("Deselect")
# Select the specified ROIs by their indices
rm.setSelectedIndexes(selected_rois)
# Save the selected ROIs to the given target path as a zip file
rm.runCommand("save selected", target)
# Deselect all ROIs again to finalize changes and maintain a clean state
rm.runCommand("Deselect")
......@@ -243,19 +323,19 @@ def select_positive_fibers( imp, channel, rm, min_intensity ):
Parameters
----------
imp : ImagePlus
the imp on which to measure
channel : integer
the channel on which to measure. starts at 1
rm : RoiManager
a reference of the IJ-RoiManager
min_intensity : integer
the selection criterion (here: intensity threshold)
imp : ij.ImagePlus
The ImagePlus on which to measure.
channel : int
The channel on which to measure. starts at 1.
rm : ij.plugin.frame.RoiManager
A reference of the IJ-RoiManager.
min_intensity : int
The selection criterion (here: intensity threshold).
Returns
-------
array
a selection of ROIs which passed the selection criterion (are above the threshold)
list
A selection of ROIs which passed the selection criterion (are above the threshold).
"""
imp.setC(channel)
all_rois = rm.getRoisAsArray()
......@@ -266,33 +346,34 @@ def select_positive_fibers( imp, channel, rm, min_intensity ):
if stats.mean > min_intensity:
selected_rois.append(i)
return selected_rois
return selected_rois
def open_rois_from_zip( rm, path ):
"""open RoiManager ROIs from zip and adds them to the RoiManager
def open_rois_from_zip(rm, path):
"""
Open ROIs from a zip file and add them to the RoiManager.
Parameters
----------
rm : RoiManager
a reference of the IJ-RoiManager
path : string
path to the ROI zip file
rm : ij.plugin.frame.RoiManager
A reference to the IJ-RoiManager.
path : str
The file path to the ROI zip file.
"""
rm.runCommand("Open", path)
def preset_results_column( rt, column, value):
"""pre-set all rows in given column of the IJ-ResultsTable with desired value
"""Pre-set all rows in given column of the IJ-ResultsTable with desired value.
Parameters
----------
rt : ResultsTable
a reference of the IJ-ResultsTable
column : string
the desired column. will be created if it does not yet exist
value : string or float or integer
the value to be set
rt : ij.measure.ResultsTable
A reference of the IJ-ResultsTable
column : str
The desired column. Will be created if it does not yet exist
value : str or float or int
The value to be set
"""
for i in range( rt.size() ):
rt.setValue(column, i, value)
......@@ -300,46 +381,52 @@ def preset_results_column( rt, column, value):
rt.show("Results")
def add_results( rt, column, row, value ):
"""adds a value in desired rows of a given column
def add_results(rt, column, row, value):
"""Add a value in specified rows of a given column.
Parameters
----------
rt : ResultsTable
a reference of the IJ-ResultsTable
column : string
the column in which to add the values
row : array
the row numbers in which too add the values.
value : string or float or integer
the value to be set
rt : ij.measure.ResultsTable
A reference to the IJ-ResultsTable.
column : str
The column in which to add the values.
row : list of int
The row numbers in which to add the values.
value : str, float, or int
The value to be set.
"""
for i in range( len( row ) ):
# Iterate over each row index in the row list
for i in range(len(row)):
# Set the specified value in the given column and row
rt.setValue(column, row[i], value)
# Display the updated ResultsTable
rt.show("Results")
def enhance_contrast( imp ):
"""use "Auto" Contrast & Brightness settings in each channel of imp
def enhance_contrast(imp):
"""Use "Auto" Contrast & Brightness settings in each channel of imp.
Parameters
----------
imp : ImagePlus
the imp on which to change C&B
imp : ij.ImagePlus
The imp on which to change C&B.
"""
for channel in range( imp.getDimensions()[2] ):
imp.setC(channel + 1) # IJ channels start at 1
for channel in range(imp.getDimensions()[2]):
imp.setC(channel + 1) # IJ channels start at 1
IJ.run(imp, "Enhance Contrast", "saturated=0.35")
def renumber_rois(rm):
"""rename all ROIs in the RoiManager according to their number
"""Rename all ROIs in the RoiManager according to their number.
The RoiManager uses 0-based indexing, so the first ROI is at index 0.
This function renames each ROI with its index (starting from 1).
Parameters
----------
rm : RoiManager
a reference of the IJ-RoiManager
rm : ij.plugin.frame.RoiManager
A reference to the IJ-RoiManager.
"""
number_of_rois = rm.getCount()
for roi in range( number_of_rois ):
......@@ -347,18 +434,28 @@ def renumber_rois(rm):
def setup_defined_ij(rm, rt):
"""set up a clean and defined Fiji user environment
"""Set up a clean and defined Fiji user environment.
This function configures the ImageJ environment to a predefined state by
resetting the RoiManager and ResultsTable, and clearing the IJ log.
Parameters
----------
rm : RoiManager
a reference of the IJ-RoiManager
rt : ResultsTable
a reference of the IJ-ResultsTable
rm : ij.plugin.frame.RoiManager
A reference to the IJ-RoiManager.
rt : ij.measure.ResultsTable
A reference to the IJ-ResultsTable.
"""
# Configure IJ options to a predefined state
fix_ij_options()
# Reset the RoiManager to remove all existing ROIs
rm.runCommand('reset')
# Reset the ResultsTable to clear all previous results
rt.reset()
# Clear the IJ log to ensure a fresh output window
IJ.log("\\Clear")
......@@ -368,6 +465,7 @@ setup_defined_ij(rm, rt)
# open image using Bio-Formats
path_to_image = fix_ij_dirs(path_to_image)
raw = open_image_with_BF(path_to_image)
raw.hide()
# get image info
raw_image_calibration = raw.getCalibration()
......@@ -383,7 +481,7 @@ if not os.path.exists( str(output_dir) ):
# open ROIS and show on image
open_rois_from_zip( rm, str(input_rois_path) )
change_all_roi_color(rm, "blue")
show_all_rois_on_image( rm, raw )
# show_all_rois_on_image( rm, raw )
# update the log for the user
IJ.log( "Now working on " + str(raw_image_title) )
......@@ -412,7 +510,7 @@ for index, fiber_channel in enumerate(all_fiber_channels):
preset_results_column( rt, "channel " + str(fiber_channel) + " positive (" + roi_colors[index] + ")", "NO" )
if all_min_fiber_intensities[index] == 0:
all_min_fiber_intensities[index] = get_threshold_from_method(raw, fiber_channel, "Mean")[0]
IJ.log( "fiber channel " + str(fiber_channel) + " intensity threshold: " + str(all_min_fiber_intensities[index]) )
IJ.log( "fiber channel " + str(fiber_channel) + " intensity threshold: " + str(all_min_fiber_intensities[index]) )
positive_fibers = select_positive_fibers( raw, fiber_channel, rm, all_min_fiber_intensities[index] )
all_fiber_subsets[index] = positive_fibers
if len(positive_fibers) > 0:
......@@ -432,29 +530,21 @@ positive_c2_c3 = list( set(all_fiber_subsets[1]).intersection(all_fiber_subsets[
positive_c1_c2_c3 = list( set(positive_c1_c2).intersection(all_fiber_subsets[2]) )
# update ROI color & results table for double and triple positives
if len(positive_c1_c2) > 0:
preset_results_column( rt, "channel " + str(fiber_channel_1) + "," + str(fiber_channel_2) + " positive (magenta)", "NO" )
change_subset_roi_color(rm, positive_c1_c2, "magenta")
save_selected_rois( rm, positive_c1_c2, output_dir + "/" + raw_image_title + "_positive_fiber_rois_c" + str(fiber_channel_1) + "_c" + str(fiber_channel_2) + ".zip")
add_results( rt, "channel " + str(fiber_channel_1) + "," + str(fiber_channel_2) + " positive (magenta)", positive_c1_c2, "YES")
if len(positive_c1_c3) > 0:
preset_results_column( rt, "channel " + str(fiber_channel_1) + "," + str(fiber_channel_3) + " positive (yellow)", "NO" )
change_subset_roi_color(rm, positive_c1_c3, "yellow")
save_selected_rois( rm, positive_c1_c3, output_dir + "/" + raw_image_title + "_positive_fiber_rois_c" + str(fiber_channel_1) + "_c" + str(fiber_channel_3) + ".zip")
add_results( rt, "channel " + str(fiber_channel_1) + "," + str(fiber_channel_3) + " positive (yellow)", positive_c1_c3, "YES")
if len(positive_c2_c3) > 0:
preset_results_column( rt, "channel " + str(fiber_channel_2) + "," + str(fiber_channel_3) + " positive (cyan)", "NO" )
change_subset_roi_color(rm, positive_c2_c3, "cyan")
save_selected_rois( rm, positive_c2_c3, output_dir + "/" + raw_image_title + "_positive_fiber_rois_c" + str(fiber_channel_2) + "_c" + str(fiber_channel_3) + ".zip")
add_results( rt, "channel " + str(fiber_channel_2) + "," + str(fiber_channel_3) + " positive (cyan)", positive_c2_c3, "YES")
if len(positive_c1_c2_c3) > 0:
preset_results_column( rt, "channel " + str(fiber_channel_1) + "," + str(fiber_channel_2) + "," + str(fiber_channel_3) + " positive(white)", "NO" )
change_subset_roi_color(rm, positive_c1_c2_c3, "white")
save_selected_rois( rm, positive_c1_c2_c3, output_dir + "/" + raw_image_title + "_positive_fiber_rois_c" + str(fiber_channel_1) + "_c" + str(fiber_channel_2) + "_c" + str(fiber_channel_3) + ".zip")
add_results( rt, "channel " + str(fiber_channel_1) + "," + str(fiber_channel_2) + "," + str(fiber_channel_3) + " positive(white)", positive_c1_c2_c3, "YES")
channels = [
(positive_c1_c2, [fiber_channel_1, fiber_channel_2], "magenta"),
(positive_c1_c3, [fiber_channel_1, fiber_channel_3], "yellow"),
(positive_c2_c3, [fiber_channel_2, fiber_channel_3], "cyan"),
(positive_c1_c2_c3, [fiber_channel_1, fiber_channel_2, fiber_channel_3], "white")
]
for positives, ch_nums, color in channels:
if positives:
ch_str = ",".join(map(str, ch_nums))
color_label = "channel %s positive (%s)" % (ch_str, color)
preset_results_column(rt, color_label.replace(',', '-'), "NO")
change_subset_roi_color(rm, positives, color)
save_selected_rois(rm, positives, "%s/%s_positive_fiber_rois_c%s.zip" % (output_dir, raw_image_title, '_c'.join(map(str, ch_nums))))
add_results(rt, color_label.replace(',', '-'), positives, "YES")
# save all results together
save_all_rois( rm, output_dir + "/" + raw_image_title + "_all_fiber_type_rois_color-coded.zip" )
......@@ -463,16 +553,16 @@ rt.save(output_dir + "/" + raw_image_title + "_fibertyping_results.csv")
# dress up the original image, save a overlay-png, present original to the user
raw.show()
show_all_rois_on_image( rm, raw )
raw.setDisplayMode(IJ.COMPOSITE)
# raw.setDisplayMode(IJ.COMPOSITE)
enhance_contrast( raw )
IJ.run("From ROI Manager", "") # ROIs -> overlays so they show up in the saved png
qc_duplicate = raw.duplicate()
IJ.saveAs(qc_duplicate, "PNG", output_dir + "/" + raw_image_title + "_fibertyping")
qc_duplicate.close()
wm.toFront( raw.getWindow() )
IJ.run("Remove Overlay", "")
raw.setDisplayMode(IJ.GRAYSCALE)
show_all_rois_on_image( rm, raw )
# IJ.run("Remove Overlay", "")
# raw.setDisplayMode(IJ.GRAYSCALE)
# show_all_rois_on_image( rm, raw )
total_execution_time_min = (time.time() - execution_start_time) / 60.0
IJ.log("total time in minutes: " + str(total_execution_time_min))
IJ.log( "~~ all done ~~" )
......
README.md
View file @ 8ad0e271
......@@ -11,9 +11,10 @@ Original code: <https://github.com/Hyojung-Choo/Myosoft/tree/Myosoft-hub>
## [`1_identify_fibers.py`](1_identify_fibers.py)
- Will identify all fibers based on the membrane staining using [Cellpose](https://github.com/MouseLand/cellpose) segmentation, filter them according to the morphometric gates and save the
corresponding ROIs.
- Need to be installed ont the machine where the script is run. Follow [this guide](https://wiki.biozentrum.unibas.ch/display/IMCF/Cellpose+python+environment) to create the environment.
- Will identify all fibers based on the membrane staining using [Cellpose](https://github.com/MouseLand/cellpose)
segmentation, filter them according to the morphometric gates and save the corresponding ROIs.
- Need to be installed on the machine where the script is run. Follow
[this guide](https://wiki.biozentrum.unibas.ch/display/IMCF/Cellpose+python+environment) to create the environment. Please don't recreate the environment if it already exists!
- Will now also save the Cellpose segmentation as a binary so it can be edited
manually. If you do so, you need to run the "extended particle analyzer"
manually as well to choose & apply the morphometric gates.
......