From c32ebcbe8c9ecc5ebcbf3f980c4694ecaa2c5568 Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Mon, 14 Apr 2025 16:32:09 +0200
Subject: [PATCH 01/26] Initial commit
Mainly copied from spots-in-fibers.py of imcftodo-1089
---
2d_spots_in_fibers.py | 768 ++++++++++++++++++++++++++++++++++++++++++
1 file changed, 768 insertions(+)
create mode 100644 2d_spots_in_fibers.py
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
new file mode 100644
index 0000000..3757c8e
--- /dev/null
+++ b/2d_spots_in_fibers.py
@@ -0,0 +1,768 @@
+#@ OpService ops
+#@ CommandService command
+#@ File (label="select image", description="select your input image", style=file) path_to_image
+#@ Integer (label="select image file series", description="leave 1 if not needed", value=1, min=1, max=20, stepSize=1, persist=false, style=slider) series_number
+#@ Integer (label="Fiber Segmentation", description="select the Fiber Segmentation RoiSet .zip file") fiber_segmentation_roiset
+#@ Integer (label="DAPI channel", description="select the DAPI channel", min=1, max=20, stepSize=1, persist=true, style=slider) dapi_channel_number
+#@ Integer (label="DAPI threshold", description="0 = Auto", min=0) threshold
+#@ String (label="processing channels", description="comma separated list of channels, e.g. 2,3,6,7", value="1,2,3,4") processing_channels_string
+#@ String (label="Spot detection quality threshold", description="comma separated list of values, one per channel", value="80,80,80,80" ) quality_thresholds_string
+
+
+# trackmate imports
+from fiji.plugin.trackmate import Settings
+from fiji.plugin.trackmate import TrackMate
+from fiji.plugin.trackmate.cellpose import CellposeDetectorFactory
+from fiji.plugin.trackmate.cellpose.CellposeSettings import PretrainedModel
+from fiji.plugin.trackmate.detection import DogDetectorFactory
+from fiji.plugin.trackmate.action import LabelImgExporter
+# ij imports
+from ij import IJ
+from ij.plugin import ZProjector, ImageCalculator
+from ij.plugin.frame import RoiManager
+from ij.measure import ResultsTable
+# Bio-Formats imports
+from loci.plugins import BF
+from loci.common import Region
+from loci.plugins.in import ImporterOptions
+from loci.formats import ImageReader, MetadataTools, Memoizer
+# MorpholibJ imports
+from inra.ijpb.binary import BinaryImages
+# CLIJ imports
+from net.haesleinhuepf.clij2 import CLIJ2
+# imglib2 imports
+from net.imglib2.img.display.imagej import ImageJFunctions
+from net.imglib2.roi import Regions
+from net.imglib2.roi.labeling import LabelRegions
+from net.imglib2.algorithm.labeling import ConnectedComponents
+# BIOP imports
+from ch.epfl.biop.ij2command import Labels2Rois
+# python imports
+import os
+
+
+def get_parentdir_filename_ext_from_path(path):
+ """ returns parent directory, filename, and file extension from a given path
+
+ Parameters
+ ----------
+ path : String
+ the full path to a file
+
+ Returns
+ -------
+ String
+ the parent directory, the filename without extension and the extension split after the dot
+ """
+ parent_dir = os.path.dirname(path)
+ base = os.path.basename(path)
+ (filename, ext) = os.path.splitext(base)
+
+ return (parent_dir, filename, ext)
+
+
+def tile_image(image_width, image_height, tile_width, tile_height, overlap):
+ """ Calculate tiles of an image of given its dimensions. Calculates tile start coordinates and tile dimensions including overlap,
+ which can directly be used in Bio-Formats "crop" function. Also calculates tile crop start coordinates and dimensions
+ to remove the overlap and the crops start coordinates to re-assemble the original size image. Useful to e.g. segment a large
+ already stitched image tile by tile.
+
+ Parameters
+ ----------
+ image_width : int
+ the input images width in pixels
+ image_height : int
+ the input images height in pixels
+ tile_width : int
+ the desired tile width in pixels
+ tile_height : int
+ the desired tile height in pixels
+ overlap : int
+ the desired tile overlap in pixels
+
+ Returns
+ -------
+ list
+ all_tile_regions: tile coordinates and dimensions including overlap
+ all_crop_regions: tile coordinates and dimensions to remove the overlap again
+ all_tile_start_no_overlap: start coordinates of the tiles without overlap to re-assemble the original size image
+ """
+ # TODO: this function likely needs refactoring to be more clear and readable
+ number_of_columns = image_width // tile_width # is a floored division
+ column_remainder_px = image_width % tile_width
+ number_of_rows = image_height // tile_height
+ row_remainder_px = image_height % tile_height
+ all_tile_regions = []
+ all_crop_regions = []
+ all_tile_start_no_overlap = []
+
+ for current_row in range(number_of_rows):
+ if current_row == number_of_rows -1 :
+ tile_height_boarder_addition = row_remainder_px # increase tile height in the last row
+ else:
+ tile_height_boarder_addition = 0
+
+ for current_column in range (number_of_columns):
+ if current_column == number_of_columns - 1 :
+ tile_width_boarder_addition = column_remainder_px # increase tile width in the last column
+ else:
+ tile_width_boarder_addition = 0
+
+ tile_start_x_no_overlap = current_column * tile_width
+ tile_start_y_no_overlap = current_row * tile_height
+
+ if current_column > 0:
+ tile_start_x = current_column * tile_width - overlap
+ crop_start_x = overlap
+ else:
+ tile_start_x = 0
+ crop_start_x = 0
+
+ if current_row > 0:
+ tile_start_y = current_row * tile_height - overlap
+ crop_start_y = overlap
+ else:
+ tile_start_y = 0
+ crop_start_y = 0
+
+ if current_column == 0 or current_column == number_of_columns - 1:
+ current_tile_width = tile_width + overlap + tile_width_boarder_addition
+ else:
+ current_tile_width = tile_width + 2 * overlap
+
+ if current_row == 0 or current_row == number_of_rows - 1:
+ current_tile_height = tile_height + overlap + tile_height_boarder_addition
+ else:
+ current_tile_height = tile_height + 2 * overlap
+
+ tile_region = [tile_start_x, tile_start_y, current_tile_width, current_tile_height]
+ crop_region = [crop_start_x, crop_start_y, current_tile_width - overlap, current_tile_height - overlap]
+ tile_start_no_overlap = [tile_start_x_no_overlap, tile_start_y_no_overlap]
+
+ all_tile_regions.append(tile_region)
+ all_crop_regions.append(crop_region)
+ all_tile_start_no_overlap.append(tile_start_no_overlap)
+
+ return all_tile_regions, all_crop_regions, all_tile_start_no_overlap
+
+
+def create_empty_image(bit_depth, image_width, image_height):
+ """creates an empty image of given dimensions. The image is 2D, filled with black pixels of value 0.
+
+ Parameters
+ ----------
+ bit_depth : int
+ the image bit dept
+ image_width : int
+ image width in px
+ image_height : int
+ image height in px
+
+ Returns
+ -------
+ ImagePlus
+ the empty image
+ """
+
+ canvas = IJ.createImage("mosaic", str(bit_depth) + "-bit black", image_width, image_height, 1)
+
+ return canvas
+
+
+def write_bf_memoryfile(path_to_file):
+ """Write a BF memo-file so subsequent access to the same file is faster.
+
+ The Bio-Formats memo-file is written next to the image file (i.e. in the
+ same folder as the given file).
+
+ Parameters
+ ----------
+ string
+ The full path to the image file.
+ """
+ reader = Memoizer(ImageReader())
+ reader.setId(path_to_file)
+ reader.close()
+
+
+def get_ome_metadata(path_to_image, series_number):
+ """Get some metadata fields using BF from an image on disk from a given series.
+ Gets number of channels, the image width, image height and bit depth.
+
+ Parameters
+ ----------
+ path_to_image : str
+ full path to the image
+ series_number : int
+ the Bio-Formats series number
+
+ Returns
+ -------
+ int
+ n_channels : the number of channels
+ int
+ image_width : the image width in px
+ int
+ image_height : the image height in px
+ int
+ bit_depth : the image bit depth
+ """
+ series_number -= 1 # python starts counting from 0
+ reader = ImageReader()
+ ome_meta = MetadataTools.createOMEXMLMetadata()
+ reader.setMetadataStore(ome_meta)
+ reader.setId(path_to_image)
+ reader.setSeries(series_number)
+ n_channels = reader.getSizeC()
+ image_width = reader.getSizeX()
+ image_height = reader.getSizeY()
+ bit_depth = reader.getBitsPerPixel()
+
+ reader.close()
+
+ return n_channels, image_width, image_height, bit_depth
+
+
+def BFopen_image(path_to_image, channel_number, series_number, region=None, z_slice_number=None):
+ """Use Bio-Formats to open a given image or subset.
+
+ Parameters
+ ----------
+ path_to_image : str
+ full path to the image file on disk
+ channel_number : int
+ the number of the channel to open
+ series_number : int
+ the Bio-Formats series number to open
+ region : list, optional
+ Bio-Formats crop region, by default None. format = [start_x, start_y, width in px, height in px]
+ z_slice_number : int, optional
+ the number of the z-slice to open, by default None
+
+ Returns
+ -------
+ ImagePlus
+ the requested image
+ """
+ series_number -= 1 # python starts counting from 0
+ channel_number -= 1 # python starts counting from 0
+ options = ImporterOptions()
+ options.setId(path_to_image)
+ options.setColorMode(ImporterOptions.COLOR_MODE_GRAYSCALE)
+ options.setSplitChannels(False)
+ options.setSplitFocalPlanes(False)
+ options.setSplitTimepoints(False)
+ options.setSeriesOn(series_number, True)
+
+ if region is not None:
+ options.setCrop(True)
+ options.setCropRegion(series_number, Region(region[0], region[1], region[2], region[3])) # x,y,w,h
+
+ options.setSpecifyRanges(True)
+ options.setCBegin(series_number, channel_number)
+ options.setCEnd(series_number, channel_number)
+ options.setCStep(series_number, 1)
+
+ if z_slice_number is not None:
+ z_slice_number -= 1 # python starts counting from 0
+ options.setZBegin(series_number, z_slice_number)
+ options.setZEnd(series_number, z_slice_number)
+ options.setZStep(series_number, 1)
+
+ imps = BF.openImagePlus(options)
+
+ return imps[0]
+
+
+def run_trackmate_dog_spot_detector(imp, quality_threshold):
+ """Run TrackMates DoG detector with a given quality threshold
+ on a target image
+
+ Parameters
+ ----------
+ imp : ImagePlus
+ the input image
+ quality_threshold : float or double
+ the spot detection quality threshold
+
+ Returns
+ -------
+ ImagePlus
+ a label image of the detected spots.
+ """
+
+ cal = imp.getCalibration()
+ settings = Settings(imp)
+
+ settings.detectorFactory = DogDetectorFactory()
+ settings.detectorSettings['DO_SUBPIXEL_LOCALIZATION'] = True
+ settings.detectorSettings['RADIUS'] = 0.15 # type = double
+ settings.detectorSettings['TARGET_CHANNEL'] = 0
+ settings.detectorSettings['THRESHOLD'] = quality_threshold # type = double
+ settings.detectorSettings['DO_MEDIAN_FILTERING'] = False
+
+ trackmate = TrackMate(settings)
+ trackmate.computeSpotFeatures(False)
+ trackmate.computeTrackFeatures(False)
+
+ if not trackmate.checkInput():
+ print( str( trackmate.getErrorMessage() ) )
+
+ if not trackmate.process():
+ print( str( trackmate.getErrorMessage() ) )
+
+ exportSpotsAsDots = True
+ exportTracksOnly = False
+ label_imp = LabelImgExporter.createLabelImagePlus(trackmate, exportSpotsAsDots, exportTracksOnly, False)
+ label_imp.setCalibration(cal)
+ imp.close()
+
+ return label_imp
+
+
+def run_trackmate_cellpose_detector(imp):
+ """Run TrackMates CellPose detector on a target image
+
+ Parameters
+ ----------
+ imp : ImagePlus
+ the input image
+
+ Returns
+ -------
+ ImagePlus
+ a label image of the detected regions.
+ """
+
+ cal = imp.getCalibration()
+ settings = Settings(imp)
+
+ # TODO: expose more parameters
+ settings.detectorFactory = CellposeDetectorFactory()
+ settings.detectorSettings['TARGET_CHANNEL'] = 0
+ settings.detectorSettings['OPTIONAL_CHANNEL_2'] = 0
+ settings.detectorSettings['CELLPOSE_PYTHON_FILEPATH'] = 'S:/cellpose_env/python.exe'
+ settings.detectorSettings['CELLPOSE_MODEL_FILEPATH'] = ''
+ settings.detectorSettings['CELLPOSE_MODEL'] = PretrainedModel.CYTO
+ settings.detectorSettings['CELL_DIAMETER'] = 30.0
+ settings.detectorSettings['USE_GPU'] = True
+ settings.detectorSettings['SIMPLIFY_CONTOURS'] = True
+
+ trackmate = TrackMate(settings)
+ trackmate.computeSpotFeatures(False)
+ trackmate.computeTrackFeatures(False)
+
+ if not trackmate.checkInput():
+ print( str( trackmate.getErrorMessage() ) )
+
+ if not trackmate.process():
+ print( str( trackmate.getErrorMessage() ) )
+
+ exportSpotsAsDots = False
+ exportTracksOnly = False
+ label_imp = LabelImgExporter.createLabelImagePlus(trackmate, exportSpotsAsDots, exportTracksOnly, False)
+ label_imp.setCalibration(cal)
+ imp.close()
+
+ return label_imp
+
+
+def get_threshold_from_method(imp, method):
+ """returns the threshold value of chosen IJ AutoThreshold method from a stack (hyperstack?)
+
+ Parameters
+ ----------
+ imp : ImagePlus (maybe also accepts ij2 dataset, img?)
+ the image from which to get the threshold value
+ method : string
+ the AutoThreshold method to use, e.g. "otsu", "yen", ...
+
+ Returns
+ -------
+ int
+ """
+ histogram = ops.run("image.histogram", imp)
+ threshold_value = ops.run("threshold.%s" % method, histogram)
+ threshold_value = int(round(threshold_value.get()))
+
+ return threshold_value
+
+
+def convert_to_binary(imp, threshold=1, scale_binary=True):
+ """Convert grayscale image to a mask / binary image
+
+ Parameters
+ ----------
+ imp : ImagePlus
+ the input image
+ threshold : int, optional
+ the threshold above which pixels are considered foreground, by default 1
+ scale_binary : bool, optional
+ scale the mask image from 0/255 to 0/1, by default True
+
+ Returns
+ -------
+ ImagePlus
+ the mask / binary image
+ """
+ mask_imp = imp.duplicate()
+ bitdepth = mask_imp.getBitDepth()
+ if bitdepth > 16.0:
+ IJ.run("Conversions...", " ")
+ IJ.run(mask_imp, "16-bit", "")
+ IJ.run("Conversions...", "scale")
+
+ IJ.setRawThreshold(mask_imp, threshold, (2**bitdepth)-1, None)
+ IJ.run(mask_imp, "Convert to Mask", "")
+ if scale_binary == True:
+ IJ.run(mask_imp, "Divide...", "value=255")
+ IJ.run(mask_imp, "Enhance Contrast", "saturated=0.35")
+ mask_imp.changes = False
+
+ return mask_imp
+
+
+def erode_labelimp_gpu(label_imp, radius, relabel_islands=True):
+ """Erode a label image on the GPU.
+
+ Parameters
+ ----------
+ label_imp : ImagePlus
+ the input image
+ radius : float
+ radius used for erosion
+ relabel_islands : bool, optional
+ if True, split objects will get new labels each , by default True
+
+ Returns
+ -------
+ ImagePlus
+ the eroded label image
+ """
+
+ clij2 = CLIJ2.getInstance()
+ labels_input = clij2.push(label_imp)
+ labels_destination = clij2.create(labels_input)
+ radius = 1.0
+ clij2.erodeLabels(labels_input, labels_destination, radius, relabel_islands)
+ eroded_labelimp = clij2.pull(labels_destination)
+ clij2.release(labels_input)
+ clij2.release(labels_destination)
+ label_imp.close()
+
+ return eroded_labelimp
+
+
+def remove_tileoverlap(imp, crop_region):
+ """Crop an image to specified dimensions.
+ The operation is destructive, the original image is lost.
+
+ Parameters
+ ----------
+ imp : ImagePlus
+ the input image
+ crop_region : list or array of int
+ the crop region in the format of [start_x, start_y, crop_width, crop_height]
+
+ Returns
+ -------
+ ImagePlus
+ the cropped image
+ """
+
+ start_x = crop_region[0]
+ start_y = crop_region[1]
+ crop_width = crop_region[2]
+ crop_height = crop_region[3]
+ imp.setRoi(start_x, start_y, crop_width, crop_height)
+ cropped_imp = imp.crop()
+ imp.close()
+
+ return cropped_imp
+
+
+def copy_and_paste_image(source, target, start_coordinates_xy):
+ """Copy the source image and paste it into the target image
+
+ Parameters
+ ----------
+ source : ImagePlus
+ the source image
+ target : ImagePlus
+ the target image
+ start_coordinates_xy : list or array of int
+ the x and y coordinates in the target image where the source image will be pasted
+ """
+ source.copy()
+ start_x = start_coordinates_xy[0]
+ start_y = start_coordinates_xy[1]
+ target.paste(start_x, start_y)
+ source.close()
+
+
+def merge_touching_labels(label_imp, bit_depth):
+ """merge touching labels in a label image so they have the same label ID.
+
+ Parameters
+ ----------
+ label_imp : ImagePlus
+ the label image with touching labels of different label ID
+ bit_depth : int
+ the image bit depth
+
+ Returns
+ -------
+ ImagePlus
+ the label image with merged touching labels
+ """
+
+ binary_imp = BinaryImages.binarize(label_imp)
+ connectivity = 8
+ merged_label_imp = BinaryImages.componentsLabeling(binary_imp, connectivity, bit_depth)
+ label_imp.close()
+ binary_imp.close()
+
+ return merged_label_imp
+
+
+def save_image_as_IJtif(imp, filename, suffix, target):
+ """Save the image as ImageJ-Tiff
+
+ Parameters
+ ----------
+ imp : ImagePlus
+ the input Image to be saved
+ filename : str
+ the image filename without extension
+ suffix : int, float or str
+ a suffix that will be added to the filename as a string
+ target : str
+ the target directory in with to save the image
+ """
+
+ savename = filename + "_" + str(suffix) + ".tif"
+ savepath = os.path.join(target, savename)
+ IJ.log("now saving: " + str(savepath))
+ IJ.saveAs(imp, "Tiff", savepath)
+
+
+def measure_label_size_shape_2d(label_imp):
+ rm = RoiManager.getInstance()
+ if not rm:
+ rm = RoiManager()
+ rm.reset()
+ rt = ResultsTable()
+
+ command.run( Labels2Rois , False , 'imp' , label_imp , 'rm', rm).get()
+ IJ.run("Set Measurements...", "area centroid perimeter shape feret's redirect=None decimal=3")
+ rm.runCommand(label_imp,"Deselect")
+ rm.runCommand(label_imp,"Measure")
+ rm.reset()
+ IJ.renameResults("Results", "Size and shape features")
+ results_table = rt.getResultsTable("Size and shape features")
+
+
+ return results_table
+
+
+def convert_labelimage_to_imglib2regions(imp):
+ """Convert a ImagePlus label image to imglib2 regions
+
+ Parameters
+ ----------
+ imp : ImagePlus
+ the input label image
+
+ Returns
+ -------
+ Imglib2 LabelRegions
+ the imglib2 label regions
+ """
+
+ # fist convert ImagePlus to img as suggested by curtis:
+ # from https://forum.image.sc/t/how-to-wrap-any-kind-of-imageplus-to-an-imglib2-img-floattype/178/6
+ wrapImg = ImageJFunctions.wrap(imp)
+ # workaround to convert a label image into an imglib2 ImgLabeling (which contains not only an image)
+ img_labeling = ops.labeling().cca(wrapImg, ConnectedComponents.StructuringElement.EIGHT_CONNECTED)
+ # img = img_labeling.getIndexImg() # the img label image
+ # ImageJFunctions.show(img)
+ regions = LabelRegions(img_labeling)
+
+ return regions
+
+
+def convert_labelimage_to_binary(label_imp, scale_binary=True):
+ """Convert a label image to a mask / binary image
+
+ Parameters
+ ----------
+ label_imp : ImagePlus
+ the input label image
+ scale_binary : bool, optional
+ scale the mask image from 0/255 to 0/1, by default True
+
+ Returns
+ -------
+ ImagePlus
+ the mask / binary image
+ """
+ binary_imp = BinaryImages.binarize(label_imp)
+ if scale_binary == True:
+ IJ.run(binary_imp, "Divide...", "value=255")
+
+ return binary_imp
+
+
+def measure_intensity_sum(label_imp, target_imp):
+ """Measure the sum intensity for each label in a label image on another target image.
+ Uses imglib2 and ops for this and works with both 2D and 3D label images.
+
+ Parameters
+ ----------
+ label_imp : ImagePlus
+ the input label image
+ target_imp : ImagePlus
+ the target image in which to measure
+
+ Returns
+ -------
+ array
+ label id and corresponding sum intensity [label_id, sum_intensity]
+ """
+ label_id = []
+ sum_intensity = []
+ target_img = ImageJFunctions.wrap(target_imp) # convert ImagePlus to img to use ops/region measurements on it
+ regions = convert_labelimage_to_imglib2regions(label_imp)
+
+ for region in regions:
+ label_id.append(region.getLabel() + 1) # region.getlabel() starts counting from 0. So the label with int 1 has the index 0.
+ input = Regions.sample(region, target_img) # returns an iterableInterval
+ sum = ops.stats().sum(input).getRealDouble()
+ sum_intensity.append(sum)
+ # other measurements see https://forum.image.sc/t/can-i-get-to-measurements-using-imagej-ops/4448/5
+ result = [label_id, sum_intensity]
+
+ return result
+
+
+def add_results_to_resultstable(results_table, column, values):
+ """Add values to the ResultsTable starting from row 0 of a given column.
+
+ Parameters
+ ----------
+ results_table : ij.measure.ResultsTable
+ a reference of the IJ-ResultsTable
+ column : string
+ the column in which to add the values
+ values : list(int, double or float)
+ array with values to be added
+ """
+ for index, value in enumerate(values):
+ results_table.setValue(column, index, value)
+
+
+def save_results_table(results_table, filename, suffix, target):
+ """Save an IJ-ResultsTable as txt to a given location
+
+ Parameters
+ ----------
+ results_table : IJ-ResultsTable
+ an IJ-ResultsTable
+ filename : str
+ filename to include in the tables name
+ suffix : str, int or float
+ a suffix to be included in the tables name
+ target : str
+ the target directory in which to save the table
+ """
+
+ savename = filename + "_" + str(suffix) + ".txt"
+ savepath = os.path.join(target, savename)
+ results_table.save(savepath)
+
+
+def save_labelimage_as_ijroiset(label_imp, filename, suffix, target):
+ """Save all labels i a label Images as IJ-ROIset to target location.
+ Only 2D, requires PTBIOP update site.
+
+ Parameters
+ ----------
+ label_imp : ImagePlus
+ the input label image
+ filename : str
+ the filename to include in the ROIset name
+ suffix : str, int or float
+ a suffix to be included in the ROIset name
+ target : str
+ the target directory in which to save the table
+ """
+ rm = RoiManager.getInstance()
+ if not rm:
+ rm = RoiManager()
+ rm.reset()
+ command.run( Labels2Rois , False , 'imp' , label_imp , 'rm', rm).get()
+ savename = filename + "_" + str(suffix) + ".zip"
+ savepath = os.path.join(target, savename)
+ rm.runCommand("Save", savepath)
+ rm.reset()
+
+
+def close_images(list_of_imps):
+ """Close given ImagePlus images
+
+ Parameters
+ ----------
+ list_of_imps : list of ImagePlus
+ list of ImagePlus images to be closed
+ """
+ for imp in list_of_imps:
+ imp.changes = False
+ imp.close()
+
+
+path_to_image = str(path_to_image).replace("\\","/")
+parent_dir, filename, ext = get_parentdir_filename_ext_from_path(path_to_image)
+write_bf_memoryfile(path_to_image)
+n_channels, image_width, image_height, bit_depth = get_ome_metadata(path_to_image, series_number)
+processing_channels_string = processing_channels_string.replace(" ", "")
+processing_channels = processing_channels_string.split(",")
+quality_thresholds_string = quality_thresholds_string.replace(" ", "")
+quality_thresholds = quality_thresholds_string.split(",")
+
+# TODO: Get the fiber segmentation and convert to labelimage
+
+# threshold DAPI channel and convert to binary
+dapi_channel = BFopen_image(path_to_image, dapi_channel_number, series_number, z_slice_number=dapi_channel_zslice)
+if threshold <= 0:
+ threshold = get_threshold_from_method(dapi_channel, "otsu")
+dapi_binary = convert_to_binary(dapi_channel, threshold)
+close_images([dapi_channel])
+
+# detect spots and count them per fiber
+results_table = ResultsTable()
+for index, channel in enumerate(processing_channels):
+ channel = int(channel)
+ quality_threshold = float(quality_thresholds[index])
+ spots_channel = BFopen_image(path_to_image, channel, series_number) # can be a stack
+ spots_label_imp = run_trackmate_dog_spot_detector(spots_channel, quality_threshold) # spot detection is 3D
+ save_image_as_IJtif(spots_label_imp, filename, "spots_ch" + str(channel), parent_dir)
+ save_labelimage_as_ijroiset(spots_label_imp, filename, "spots_ch" + str(channel), parent_dir)
+ spots_binary_imp = convert_labelimage_to_binary(spots_label_imp) # can be a stack
+ spots_binary_imp_sum_proj = ZProjector.run(spots_binary_imp, "sum") # if 2 (n) spots perfecly overlap in z, the pixel value will be 2 (n)
+ dapi_positive_spots_binary = ImageCalculator.run(spots_binary_imp_sum_proj, dapi_binary, "Multiply create")
+ dapi_negative_spots_binary = ImageCalculator.run(spots_binary_imp_sum_proj, dapi_positive_spots_binary, "Subtract create")
+
+ n_spots_per_fiber = measure_intensity_sum(fibers_label_imp, spots_binary_imp_sum_proj)
+ n_dapi_positive_spots_per_fiber = measure_intensity_sum(fibers_label_imp, dapi_positive_spots_binary)
+ n_dapi_negative_spots_per_fiber = measure_intensity_sum(fibers_label_imp, dapi_negative_spots_binary)
+
+ # TODO: the column fiber label ID needs to be added only one time. Maybe check before if column exists.
+ add_results_to_resultstable(results_table, "fiber label ID", n_spots_per_fiber[0])
+ add_results_to_resultstable(results_table, "n spots channel " + str(channel), n_spots_per_fiber[1])
+ add_results_to_resultstable(results_table, "n spots dapi positive channel " + str(channel), n_dapi_positive_spots_per_fiber[1])
+ add_results_to_resultstable(results_table, "n spots dapi negative channel " + str(channel), n_dapi_negative_spots_per_fiber[1])
+ close_images([spots_channel, spots_label_imp, spots_binary_imp, spots_binary_imp_sum_proj, dapi_binary, dapi_positive_spots_binary, dapi_negative_spots_binary])
+
+results_table.show("Spots")
+save_results_table(results_table, filename, "Spots", parent_dir)
+IJ.log("DONE")
\ No newline at end of file
--
GitLab
From d8310623759b2be3866c2d7b499c5e8d618c9f89 Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Mon, 14 Apr 2025 17:15:20 +0200
Subject: [PATCH 02/26] Add function to convert ijrois to labelimage
---
2d_spots_in_fibers.py | 29 ++++++++++++++++++++++++++++-
1 file changed, 28 insertions(+), 1 deletion(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index 3757c8e..a5b54fe 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -36,7 +36,7 @@ from net.imglib2.roi import Regions
from net.imglib2.roi.labeling import LabelRegions
from net.imglib2.algorithm.labeling import ConnectedComponents
# BIOP imports
-from ch.epfl.biop.ij2command import Labels2Rois
+from ch.epfl.biop.ij2command import Labels2Rois, Rois2Labels
# python imports
import os
@@ -707,6 +707,33 @@ def save_labelimage_as_ijroiset(label_imp, filename, suffix, target):
rm.reset()
+def load_rois_from_zip(path):
+ """Load ROIs from the given zip file and add them to the RoiManager.
+
+ Parameters
+ ----------
+ path : string
+ Path to the ROI zip file.
+ """
+ rm = RoiManager.getInstance()
+ if not rm:
+ rm = RoiManager()
+ rm.reset()
+
+ rm.runCommand("Open", path)
+
+
+def convert_rois_to_labelimage(imp):
+ rm = RoiManager.getInstance()
+ if not rm:
+ rm = RoiManager()
+
+ label_imp = command.run( Rois2Labels , False , 'imp' , imp , 'rm', rm).get().getOutput("label_imp")
+ rm.reset() # TODO: should be optional but can be default
+
+ return label_imp
+
+
def close_images(list_of_imps):
"""Close given ImagePlus images
--
GitLab
From 005655c760979b82b0cb73539698e1d6e7996d87 Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Mon, 14 Apr 2025 17:16:07 +0200
Subject: [PATCH 03/26] Get path to ij roiset from GUI
---
2d_spots_in_fibers.py | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index a5b54fe..08f87b6 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -2,7 +2,7 @@
#@ CommandService command
#@ File (label="select image", description="select your input image", style=file) path_to_image
#@ Integer (label="select image file series", description="leave 1 if not needed", value=1, min=1, max=20, stepSize=1, persist=false, style=slider) series_number
-#@ Integer (label="Fiber Segmentation", description="select the Fiber Segmentation RoiSet .zip file") fiber_segmentation_roiset
+#@ File (label="Fiber Segmentation", description="select the Fiber Segmentation RoiSet .zip file", style=file) fiber_segmentation_roiset
#@ Integer (label="DAPI channel", description="select the DAPI channel", min=1, max=20, stepSize=1, persist=true, style=slider) dapi_channel_number
#@ Integer (label="DAPI threshold", description="0 = Auto", min=0) threshold
#@ String (label="processing channels", description="comma separated list of channels, e.g. 2,3,6,7", value="1,2,3,4") processing_channels_string
@@ -748,6 +748,7 @@ def close_images(list_of_imps):
path_to_image = str(path_to_image).replace("\\","/")
+fiber_segmentation_roiset = str(fiber_segmentation_roiset).replace("\\","/")
parent_dir, filename, ext = get_parentdir_filename_ext_from_path(path_to_image)
write_bf_memoryfile(path_to_image)
n_channels, image_width, image_height, bit_depth = get_ome_metadata(path_to_image, series_number)
--
GitLab
From f6b804c8a44a8a797da9cade12b284bb5635b220 Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Mon, 14 Apr 2025 17:17:16 +0200
Subject: [PATCH 04/26] Create Labelimage from ij roiset
---
2d_spots_in_fibers.py | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index 08f87b6..53df4a2 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -757,7 +757,12 @@ processing_channels = processing_channels_string.split(",")
quality_thresholds_string = quality_thresholds_string.replace(" ", "")
quality_thresholds = quality_thresholds_string.split(",")
-# TODO: Get the fiber segmentation and convert to labelimage
+# Get the fiber segmentation and convert to labelimage
+canvas = create_empty_image(32, image_width, image_height)
+load_rois_from_zip(fiber_segmentation_roiset)
+fiber_label_imp = convert_rois_to_labelimage(canvas)
+canvas.close()
+fiber_label_imp.show()
# threshold DAPI channel and convert to binary
dapi_channel = BFopen_image(path_to_image, dapi_channel_number, series_number, z_slice_number=dapi_channel_zslice)
--
GitLab
From 9a094bcc63e6ef72096c4269550d2c97ae6cc9cf Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Mon, 14 Apr 2025 17:18:48 +0200
Subject: [PATCH 05/26] Don't use z-slice option, input is a MIP
---
2d_spots_in_fibers.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index 53df4a2..41ca9e4 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -765,7 +765,7 @@ canvas.close()
fiber_label_imp.show()
# threshold DAPI channel and convert to binary
-dapi_channel = BFopen_image(path_to_image, dapi_channel_number, series_number, z_slice_number=dapi_channel_zslice)
+dapi_channel = BFopen_image(path_to_image, dapi_channel_number, series_number)
if threshold <= 0:
threshold = get_threshold_from_method(dapi_channel, "otsu")
dapi_binary = convert_to_binary(dapi_channel, threshold)
--
GitLab
From 106d690d5b4c1a92e40ca840596291315984d1ec Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Mon, 14 Apr 2025 17:32:17 +0200
Subject: [PATCH 06/26] Remove sum projection as data is a 2D MIP
---
2d_spots_in_fibers.py | 15 +++++++--------
1 file changed, 7 insertions(+), 8 deletions(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index 41ca9e4..23751d0 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -776,16 +776,15 @@ results_table = ResultsTable()
for index, channel in enumerate(processing_channels):
channel = int(channel)
quality_threshold = float(quality_thresholds[index])
- spots_channel = BFopen_image(path_to_image, channel, series_number) # can be a stack
- spots_label_imp = run_trackmate_dog_spot_detector(spots_channel, quality_threshold) # spot detection is 3D
+ spots_channel = BFopen_image(path_to_image, channel, series_number)
+ spots_label_imp = run_trackmate_dog_spot_detector(spots_channel, quality_threshold)
save_image_as_IJtif(spots_label_imp, filename, "spots_ch" + str(channel), parent_dir)
save_labelimage_as_ijroiset(spots_label_imp, filename, "spots_ch" + str(channel), parent_dir)
- spots_binary_imp = convert_labelimage_to_binary(spots_label_imp) # can be a stack
- spots_binary_imp_sum_proj = ZProjector.run(spots_binary_imp, "sum") # if 2 (n) spots perfecly overlap in z, the pixel value will be 2 (n)
- dapi_positive_spots_binary = ImageCalculator.run(spots_binary_imp_sum_proj, dapi_binary, "Multiply create")
- dapi_negative_spots_binary = ImageCalculator.run(spots_binary_imp_sum_proj, dapi_positive_spots_binary, "Subtract create")
+ spots_binary_imp = convert_labelimage_to_binary(spots_label_imp)
+ dapi_positive_spots_binary = ImageCalculator.run(spots_binary_imp, dapi_binary, "Multiply create")
+ dapi_negative_spots_binary = ImageCalculator.run(spots_binary_imp, dapi_positive_spots_binary, "Subtract create")
- n_spots_per_fiber = measure_intensity_sum(fibers_label_imp, spots_binary_imp_sum_proj)
+ n_spots_per_fiber = measure_intensity_sum(fibers_label_imp, spots_binary_imp)
n_dapi_positive_spots_per_fiber = measure_intensity_sum(fibers_label_imp, dapi_positive_spots_binary)
n_dapi_negative_spots_per_fiber = measure_intensity_sum(fibers_label_imp, dapi_negative_spots_binary)
@@ -794,7 +793,7 @@ for index, channel in enumerate(processing_channels):
add_results_to_resultstable(results_table, "n spots channel " + str(channel), n_spots_per_fiber[1])
add_results_to_resultstable(results_table, "n spots dapi positive channel " + str(channel), n_dapi_positive_spots_per_fiber[1])
add_results_to_resultstable(results_table, "n spots dapi negative channel " + str(channel), n_dapi_negative_spots_per_fiber[1])
- close_images([spots_channel, spots_label_imp, spots_binary_imp, spots_binary_imp_sum_proj, dapi_binary, dapi_positive_spots_binary, dapi_negative_spots_binary])
+ close_images([spots_channel, spots_label_imp, spots_binary_imp, spots_binary_imp, dapi_binary, dapi_positive_spots_binary, dapi_negative_spots_binary])
results_table.show("Spots")
save_results_table(results_table, filename, "Spots", parent_dir)
--
GitLab
From db261db207c53f5d2ab718801dce70d818e5f024 Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Mon, 14 Apr 2025 17:32:40 +0200
Subject: [PATCH 07/26] Do not show intermediate image
---
2d_spots_in_fibers.py | 1 -
1 file changed, 1 deletion(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index 23751d0..ae047bd 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -762,7 +762,6 @@ canvas = create_empty_image(32, image_width, image_height)
load_rois_from_zip(fiber_segmentation_roiset)
fiber_label_imp = convert_rois_to_labelimage(canvas)
canvas.close()
-fiber_label_imp.show()
# threshold DAPI channel and convert to binary
dapi_channel = BFopen_image(path_to_image, dapi_channel_number, series_number)
--
GitLab
From 811cdd7425ba30df15c2bba0efb331f293900063 Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Mon, 14 Apr 2025 17:32:51 +0200
Subject: [PATCH 08/26] Precises comment
---
2d_spots_in_fibers.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index ae047bd..f16d7c7 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -757,10 +757,10 @@ processing_channels = processing_channels_string.split(",")
quality_thresholds_string = quality_thresholds_string.replace(" ", "")
quality_thresholds = quality_thresholds_string.split(",")
-# Get the fiber segmentation and convert to labelimage
+# Get the fiber segmentation from ij roizip and convert to labelimage
canvas = create_empty_image(32, image_width, image_height)
load_rois_from_zip(fiber_segmentation_roiset)
-fiber_label_imp = convert_rois_to_labelimage(canvas)
+fibers_label_imp = convert_rois_to_labelimage(canvas)
canvas.close()
# threshold DAPI channel and convert to binary
--
GitLab
From d6ed724d72bf72a7bf67d3aefbe941e93c882ffc Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Tue, 15 Apr 2025 11:11:11 +0200
Subject: [PATCH 09/26] Adapt to api change in trackmate
---
2d_spots_in_fibers.py | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index f16d7c7..6dffdfc 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -313,7 +313,8 @@ def run_trackmate_dog_spot_detector(imp, quality_threshold):
exportSpotsAsDots = True
exportTracksOnly = False
- label_imp = LabelImgExporter.createLabelImagePlus(trackmate, exportSpotsAsDots, exportTracksOnly, False)
+ labelIdPainting = LabelImgExporter.LabelIdPainting.LABEL_IS_SPOT_ID
+ label_imp = LabelImgExporter.createLabelImagePlus(trackmate, exportSpotsAsDots, exportTracksOnly, labelIdPainting)
label_imp.setCalibration(cal)
imp.close()
--
GitLab
From 48234c5bd687e0ad1871df95c1071909e31cdb30 Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Tue, 15 Apr 2025 11:12:34 +0200
Subject: [PATCH 10/26] Add minimun spot diameter as parameter
---
2d_spots_in_fibers.py | 18 ++++++++----------
1 file changed, 8 insertions(+), 10 deletions(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index 6dffdfc..3d169ac 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -7,7 +7,7 @@
#@ Integer (label="DAPI threshold", description="0 = Auto", min=0) threshold
#@ String (label="processing channels", description="comma separated list of channels, e.g. 2,3,6,7", value="1,2,3,4") processing_channels_string
#@ String (label="Spot detection quality threshold", description="comma separated list of values, one per channel", value="80,80,80,80" ) quality_thresholds_string
-
+#@ Double (label="Minimum spot diameter", description="smaller spots will be discarded, value=5, min=1, max=200, stepSize=0.5, persist=false, style=slider) spot_diameter
# trackmate imports
from fiji.plugin.trackmate import Settings
@@ -274,7 +274,7 @@ def BFopen_image(path_to_image, channel_number, series_number, region=None, z_sl
return imps[0]
-def run_trackmate_dog_spot_detector(imp, quality_threshold):
+def run_trackmate_dog_spot_detector(imp, spot_diameter, quality_threshold):
"""Run TrackMates DoG detector with a given quality threshold
on a target image
@@ -296,7 +296,7 @@ def run_trackmate_dog_spot_detector(imp, quality_threshold):
settings.detectorFactory = DogDetectorFactory()
settings.detectorSettings['DO_SUBPIXEL_LOCALIZATION'] = True
- settings.detectorSettings['RADIUS'] = 0.15 # type = double
+ settings.detectorSettings['RADIUS'] = spot_diameter / 2 # type = double
settings.detectorSettings['TARGET_CHANNEL'] = 0
settings.detectorSettings['THRESHOLD'] = quality_threshold # type = double
settings.detectorSettings['DO_MEDIAN_FILTERING'] = False
@@ -758,18 +758,16 @@ processing_channels = processing_channels_string.split(",")
quality_thresholds_string = quality_thresholds_string.replace(" ", "")
quality_thresholds = quality_thresholds_string.split(",")
-# Get the fiber segmentation from ij roizip and convert to labelimage
-canvas = create_empty_image(32, image_width, image_height)
-load_rois_from_zip(fiber_segmentation_roiset)
-fibers_label_imp = convert_rois_to_labelimage(canvas)
-canvas.close()
-
# threshold DAPI channel and convert to binary
dapi_channel = BFopen_image(path_to_image, dapi_channel_number, series_number)
if threshold <= 0:
threshold = get_threshold_from_method(dapi_channel, "otsu")
dapi_binary = convert_to_binary(dapi_channel, threshold)
-close_images([dapi_channel])
+
+# Get the fiber segmentation from ij roizip and convert to labelimage
+load_rois_from_zip(fiber_segmentation_roiset)
+fibers_label_imp = convert_rois_to_labelimage(dapi_channel)
+dapi_channel.close()
# detect spots and count them per fiber
results_table = ResultsTable()
--
GitLab
From d598275083a8f64f1a0bb84a6223d65abad6b67f Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Tue, 15 Apr 2025 11:42:09 +0200
Subject: [PATCH 11/26] Remove unused functions and imports
---
2d_spots_in_fibers.py | 283 +-----------------------------------------
1 file changed, 1 insertion(+), 282 deletions(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index 3d169ac..0319dd4 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -12,13 +12,11 @@
# trackmate imports
from fiji.plugin.trackmate import Settings
from fiji.plugin.trackmate import TrackMate
-from fiji.plugin.trackmate.cellpose import CellposeDetectorFactory
-from fiji.plugin.trackmate.cellpose.CellposeSettings import PretrainedModel
from fiji.plugin.trackmate.detection import DogDetectorFactory
from fiji.plugin.trackmate.action import LabelImgExporter
# ij imports
from ij import IJ
-from ij.plugin import ZProjector, ImageCalculator
+from ij.plugin import ImageCalculator
from ij.plugin.frame import RoiManager
from ij.measure import ResultsTable
# Bio-Formats imports
@@ -28,8 +26,6 @@ from loci.plugins.in import ImporterOptions
from loci.formats import ImageReader, MetadataTools, Memoizer
# MorpholibJ imports
from inra.ijpb.binary import BinaryImages
-# CLIJ imports
-from net.haesleinhuepf.clij2 import CLIJ2
# imglib2 imports
from net.imglib2.img.display.imagej import ImageJFunctions
from net.imglib2.roi import Regions
@@ -61,114 +57,6 @@ def get_parentdir_filename_ext_from_path(path):
return (parent_dir, filename, ext)
-def tile_image(image_width, image_height, tile_width, tile_height, overlap):
- """ Calculate tiles of an image of given its dimensions. Calculates tile start coordinates and tile dimensions including overlap,
- which can directly be used in Bio-Formats "crop" function. Also calculates tile crop start coordinates and dimensions
- to remove the overlap and the crops start coordinates to re-assemble the original size image. Useful to e.g. segment a large
- already stitched image tile by tile.
-
- Parameters
- ----------
- image_width : int
- the input images width in pixels
- image_height : int
- the input images height in pixels
- tile_width : int
- the desired tile width in pixels
- tile_height : int
- the desired tile height in pixels
- overlap : int
- the desired tile overlap in pixels
-
- Returns
- -------
- list
- all_tile_regions: tile coordinates and dimensions including overlap
- all_crop_regions: tile coordinates and dimensions to remove the overlap again
- all_tile_start_no_overlap: start coordinates of the tiles without overlap to re-assemble the original size image
- """
- # TODO: this function likely needs refactoring to be more clear and readable
- number_of_columns = image_width // tile_width # is a floored division
- column_remainder_px = image_width % tile_width
- number_of_rows = image_height // tile_height
- row_remainder_px = image_height % tile_height
- all_tile_regions = []
- all_crop_regions = []
- all_tile_start_no_overlap = []
-
- for current_row in range(number_of_rows):
- if current_row == number_of_rows -1 :
- tile_height_boarder_addition = row_remainder_px # increase tile height in the last row
- else:
- tile_height_boarder_addition = 0
-
- for current_column in range (number_of_columns):
- if current_column == number_of_columns - 1 :
- tile_width_boarder_addition = column_remainder_px # increase tile width in the last column
- else:
- tile_width_boarder_addition = 0
-
- tile_start_x_no_overlap = current_column * tile_width
- tile_start_y_no_overlap = current_row * tile_height
-
- if current_column > 0:
- tile_start_x = current_column * tile_width - overlap
- crop_start_x = overlap
- else:
- tile_start_x = 0
- crop_start_x = 0
-
- if current_row > 0:
- tile_start_y = current_row * tile_height - overlap
- crop_start_y = overlap
- else:
- tile_start_y = 0
- crop_start_y = 0
-
- if current_column == 0 or current_column == number_of_columns - 1:
- current_tile_width = tile_width + overlap + tile_width_boarder_addition
- else:
- current_tile_width = tile_width + 2 * overlap
-
- if current_row == 0 or current_row == number_of_rows - 1:
- current_tile_height = tile_height + overlap + tile_height_boarder_addition
- else:
- current_tile_height = tile_height + 2 * overlap
-
- tile_region = [tile_start_x, tile_start_y, current_tile_width, current_tile_height]
- crop_region = [crop_start_x, crop_start_y, current_tile_width - overlap, current_tile_height - overlap]
- tile_start_no_overlap = [tile_start_x_no_overlap, tile_start_y_no_overlap]
-
- all_tile_regions.append(tile_region)
- all_crop_regions.append(crop_region)
- all_tile_start_no_overlap.append(tile_start_no_overlap)
-
- return all_tile_regions, all_crop_regions, all_tile_start_no_overlap
-
-
-def create_empty_image(bit_depth, image_width, image_height):
- """creates an empty image of given dimensions. The image is 2D, filled with black pixels of value 0.
-
- Parameters
- ----------
- bit_depth : int
- the image bit dept
- image_width : int
- image width in px
- image_height : int
- image height in px
-
- Returns
- -------
- ImagePlus
- the empty image
- """
-
- canvas = IJ.createImage("mosaic", str(bit_depth) + "-bit black", image_width, image_height, 1)
-
- return canvas
-
-
def write_bf_memoryfile(path_to_file):
"""Write a BF memo-file so subsequent access to the same file is faster.
@@ -321,53 +209,6 @@ def run_trackmate_dog_spot_detector(imp, spot_diameter, quality_threshold):
return label_imp
-def run_trackmate_cellpose_detector(imp):
- """Run TrackMates CellPose detector on a target image
-
- Parameters
- ----------
- imp : ImagePlus
- the input image
-
- Returns
- -------
- ImagePlus
- a label image of the detected regions.
- """
-
- cal = imp.getCalibration()
- settings = Settings(imp)
-
- # TODO: expose more parameters
- settings.detectorFactory = CellposeDetectorFactory()
- settings.detectorSettings['TARGET_CHANNEL'] = 0
- settings.detectorSettings['OPTIONAL_CHANNEL_2'] = 0
- settings.detectorSettings['CELLPOSE_PYTHON_FILEPATH'] = 'S:/cellpose_env/python.exe'
- settings.detectorSettings['CELLPOSE_MODEL_FILEPATH'] = ''
- settings.detectorSettings['CELLPOSE_MODEL'] = PretrainedModel.CYTO
- settings.detectorSettings['CELL_DIAMETER'] = 30.0
- settings.detectorSettings['USE_GPU'] = True
- settings.detectorSettings['SIMPLIFY_CONTOURS'] = True
-
- trackmate = TrackMate(settings)
- trackmate.computeSpotFeatures(False)
- trackmate.computeTrackFeatures(False)
-
- if not trackmate.checkInput():
- print( str( trackmate.getErrorMessage() ) )
-
- if not trackmate.process():
- print( str( trackmate.getErrorMessage() ) )
-
- exportSpotsAsDots = False
- exportTracksOnly = False
- label_imp = LabelImgExporter.createLabelImagePlus(trackmate, exportSpotsAsDots, exportTracksOnly, False)
- label_imp.setCalibration(cal)
- imp.close()
-
- return label_imp
-
-
def get_threshold_from_method(imp, method):
"""returns the threshold value of chosen IJ AutoThreshold method from a stack (hyperstack?)
@@ -423,109 +264,6 @@ def convert_to_binary(imp, threshold=1, scale_binary=True):
return mask_imp
-def erode_labelimp_gpu(label_imp, radius, relabel_islands=True):
- """Erode a label image on the GPU.
-
- Parameters
- ----------
- label_imp : ImagePlus
- the input image
- radius : float
- radius used for erosion
- relabel_islands : bool, optional
- if True, split objects will get new labels each , by default True
-
- Returns
- -------
- ImagePlus
- the eroded label image
- """
-
- clij2 = CLIJ2.getInstance()
- labels_input = clij2.push(label_imp)
- labels_destination = clij2.create(labels_input)
- radius = 1.0
- clij2.erodeLabels(labels_input, labels_destination, radius, relabel_islands)
- eroded_labelimp = clij2.pull(labels_destination)
- clij2.release(labels_input)
- clij2.release(labels_destination)
- label_imp.close()
-
- return eroded_labelimp
-
-
-def remove_tileoverlap(imp, crop_region):
- """Crop an image to specified dimensions.
- The operation is destructive, the original image is lost.
-
- Parameters
- ----------
- imp : ImagePlus
- the input image
- crop_region : list or array of int
- the crop region in the format of [start_x, start_y, crop_width, crop_height]
-
- Returns
- -------
- ImagePlus
- the cropped image
- """
-
- start_x = crop_region[0]
- start_y = crop_region[1]
- crop_width = crop_region[2]
- crop_height = crop_region[3]
- imp.setRoi(start_x, start_y, crop_width, crop_height)
- cropped_imp = imp.crop()
- imp.close()
-
- return cropped_imp
-
-
-def copy_and_paste_image(source, target, start_coordinates_xy):
- """Copy the source image and paste it into the target image
-
- Parameters
- ----------
- source : ImagePlus
- the source image
- target : ImagePlus
- the target image
- start_coordinates_xy : list or array of int
- the x and y coordinates in the target image where the source image will be pasted
- """
- source.copy()
- start_x = start_coordinates_xy[0]
- start_y = start_coordinates_xy[1]
- target.paste(start_x, start_y)
- source.close()
-
-
-def merge_touching_labels(label_imp, bit_depth):
- """merge touching labels in a label image so they have the same label ID.
-
- Parameters
- ----------
- label_imp : ImagePlus
- the label image with touching labels of different label ID
- bit_depth : int
- the image bit depth
-
- Returns
- -------
- ImagePlus
- the label image with merged touching labels
- """
-
- binary_imp = BinaryImages.binarize(label_imp)
- connectivity = 8
- merged_label_imp = BinaryImages.componentsLabeling(binary_imp, connectivity, bit_depth)
- label_imp.close()
- binary_imp.close()
-
- return merged_label_imp
-
-
def save_image_as_IJtif(imp, filename, suffix, target):
"""Save the image as ImageJ-Tiff
@@ -547,25 +285,6 @@ def save_image_as_IJtif(imp, filename, suffix, target):
IJ.saveAs(imp, "Tiff", savepath)
-def measure_label_size_shape_2d(label_imp):
- rm = RoiManager.getInstance()
- if not rm:
- rm = RoiManager()
- rm.reset()
- rt = ResultsTable()
-
- command.run( Labels2Rois , False , 'imp' , label_imp , 'rm', rm).get()
- IJ.run("Set Measurements...", "area centroid perimeter shape feret's redirect=None decimal=3")
- rm.runCommand(label_imp,"Deselect")
- rm.runCommand(label_imp,"Measure")
- rm.reset()
- IJ.renameResults("Results", "Size and shape features")
- results_table = rt.getResultsTable("Size and shape features")
-
-
- return results_table
-
-
def convert_labelimage_to_imglib2regions(imp):
"""Convert a ImagePlus label image to imglib2 regions
--
GitLab
From 80ed315b5c8e43787fbee0c1ac40016871e0a584 Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Tue, 15 Apr 2025 11:44:04 +0200
Subject: [PATCH 12/26] Fix syntax error
---
2d_spots_in_fibers.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index 0319dd4..736d494 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -7,7 +7,7 @@
#@ Integer (label="DAPI threshold", description="0 = Auto", min=0) threshold
#@ String (label="processing channels", description="comma separated list of channels, e.g. 2,3,6,7", value="1,2,3,4") processing_channels_string
#@ String (label="Spot detection quality threshold", description="comma separated list of values, one per channel", value="80,80,80,80" ) quality_thresholds_string
-#@ Double (label="Minimum spot diameter", description="smaller spots will be discarded, value=5, min=1, max=200, stepSize=0.5, persist=false, style=slider) spot_diameter
+#@ Double (label="Minimum spot diameter", description="smaller spots will be discarded", value=5, min=1, max=200, stepSize=0.5, persist=false) spot_diameter
# trackmate imports
from fiji.plugin.trackmate import Settings
--
GitLab
From 34beb9c2f2132d25faa9a84327fa778e90534f2b Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Tue, 15 Apr 2025 16:40:02 +0200
Subject: [PATCH 13/26] Change spot label ID painting method
---
2d_spots_in_fibers.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index 736d494..4f51642 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -201,7 +201,7 @@ def run_trackmate_dog_spot_detector(imp, spot_diameter, quality_threshold):
exportSpotsAsDots = True
exportTracksOnly = False
- labelIdPainting = LabelImgExporter.LabelIdPainting.LABEL_IS_SPOT_ID
+ labelIdPainting = LabelImgExporter.LabelIdPainting.LABEL_IS_INDEX_MOVIE_UNIQUE
label_imp = LabelImgExporter.createLabelImagePlus(trackmate, exportSpotsAsDots, exportTracksOnly, labelIdPainting)
label_imp.setCalibration(cal)
imp.close()
--
GitLab
From f1669c5c2bdd42fd74f907b1268396a8099e2be3 Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Tue, 15 Apr 2025 16:40:32 +0200
Subject: [PATCH 14/26] set default spot diameter to 0.3
---
2d_spots_in_fibers.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index 4f51642..0c42fbf 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -7,7 +7,7 @@
#@ Integer (label="DAPI threshold", description="0 = Auto", min=0) threshold
#@ String (label="processing channels", description="comma separated list of channels, e.g. 2,3,6,7", value="1,2,3,4") processing_channels_string
#@ String (label="Spot detection quality threshold", description="comma separated list of values, one per channel", value="80,80,80,80" ) quality_thresholds_string
-#@ Double (label="Minimum spot diameter", description="smaller spots will be discarded", value=5, min=1, max=200, stepSize=0.5, persist=false) spot_diameter
+#@ Double (label="Minimum spot diameter", description="smaller spots will be discarded", value=0.3, min=1, max=10, stepSize=0.1) spot_diameter
# trackmate imports
from fiji.plugin.trackmate import Settings
--
GitLab
From 352cb1c9ed28a0b93d83f921a2db65d3f7c6f095 Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Tue, 15 Apr 2025 16:41:11 +0200
Subject: [PATCH 15/26] Add missing spot diameter parameter to function
---
2d_spots_in_fibers.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index 0c42fbf..2bbd1e5 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -494,7 +494,7 @@ for index, channel in enumerate(processing_channels):
channel = int(channel)
quality_threshold = float(quality_thresholds[index])
spots_channel = BFopen_image(path_to_image, channel, series_number)
- spots_label_imp = run_trackmate_dog_spot_detector(spots_channel, quality_threshold)
+ spots_label_imp = run_trackmate_dog_spot_detector(spots_channel, spot_diameter, quality_threshold)
save_image_as_IJtif(spots_label_imp, filename, "spots_ch" + str(channel), parent_dir)
save_labelimage_as_ijroiset(spots_label_imp, filename, "spots_ch" + str(channel), parent_dir)
spots_binary_imp = convert_labelimage_to_binary(spots_label_imp)
--
GitLab
From f202930ed32d4dc81f2b1b6ef62373cf00a808cb Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Tue, 15 Apr 2025 16:41:26 +0200
Subject: [PATCH 16/26] Run Garbage Collector at the end of the script
---
2d_spots_in_fibers.py | 1 +
1 file changed, 1 insertion(+)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index 2bbd1e5..9fd778b 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -514,4 +514,5 @@ for index, channel in enumerate(processing_channels):
results_table.show("Spots")
save_results_table(results_table, filename, "Spots", parent_dir)
+IJ.run("Collect Garbage", "");
IJ.log("DONE")
\ No newline at end of file
--
GitLab
From f21b7d89b59e0b66d347b96b1b1ceac9ae017e5e Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Wed, 16 Apr 2025 10:01:33 +0200
Subject: [PATCH 17/26] Remove unnecessary semicolon
---
2d_spots_in_fibers.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index 9fd778b..fff2206 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -514,5 +514,5 @@ for index, channel in enumerate(processing_channels):
results_table.show("Spots")
save_results_table(results_table, filename, "Spots", parent_dir)
-IJ.run("Collect Garbage", "");
+IJ.run("Collect Garbage", "")
IJ.log("DONE")
\ No newline at end of file
--
GitLab
From fa02df7242365117df2b34aaf98102700388e6bc Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Wed, 16 Apr 2025 10:01:52 +0200
Subject: [PATCH 18/26] Add TODO
---
2d_spots_in_fibers.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index fff2206..510df1e 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -332,7 +332,7 @@ def convert_labelimage_to_binary(label_imp, scale_binary=True):
return binary_imp
-
+# TODO: test simpler way using IJ roi measure
def measure_intensity_sum(label_imp, target_imp):
"""Measure the sum intensity for each label in a label image on another target image.
Uses imglib2 and ops for this and works with both 2D and 3D label images.
--
GitLab
From e3e5ee7656b30d566039f0d8f0f1737add6f5466 Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Wed, 16 Apr 2025 10:12:16 +0200
Subject: [PATCH 19/26] Remove unused function and imports
---
2d_spots_in_fibers.py | 58 +++++++++++++++++++++++++++----------------
1 file changed, 37 insertions(+), 21 deletions(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index 510df1e..181b435 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -1,5 +1,6 @@
#@ OpService ops
#@ CommandService command
+#@ RoiManager rm
#@ File (label="select image", description="select your input image", style=file) path_to_image
#@ Integer (label="select image file series", description="leave 1 if not needed", value=1, min=1, max=20, stepSize=1, persist=false, style=slider) series_number
#@ File (label="Fiber Segmentation", description="select the Fiber Segmentation RoiSet .zip file", style=file) fiber_segmentation_roiset
@@ -19,6 +20,8 @@ from ij import IJ
from ij.plugin import ImageCalculator
from ij.plugin.frame import RoiManager
from ij.measure import ResultsTable
+from ij.measure import Measurements as M
+from ij.plugin.filter import Analyzer
# Bio-Formats imports
from loci.plugins import BF
from loci.common import Region
@@ -332,37 +335,50 @@ def convert_labelimage_to_binary(label_imp, scale_binary=True):
return binary_imp
-# TODO: test simpler way using IJ roi measure
-def measure_intensity_sum(label_imp, target_imp):
- """Measure the sum intensity for each label in a label image on another target image.
- Uses imglib2 and ops for this and works with both 2D and 3D label images.
+
+def measure_intensity_sum(imp, rm):
+ """
+ Measure theraw integrated intensity for all rois in target imp.
Parameters
----------
- label_imp : ImagePlus
- the input label image
- target_imp : ImagePlus
- the target image in which to measure
+ imp : ImagePlus
+ The image from which the intensity will be measured.
+ rm : RoiManager
+ The ROI Manager containing the regions of interest to be analyzed.
Returns
-------
- array
- label id and corresponding sum intensity [label_id, sum_intensity]
+ label_id : list of str
+ A list of labels corresponding to each ROI.
+ sum_intensity : list of int
+ A list of summed integrated intensities for each ROI.
+
+ Notes
+ -----
+ The results are stored in a `ij.ResultsTable`,
+ from which the raw integrated density values are extracted.
+
+ Example
+ -------
+ >>> labels, intensities = measure_intensity_sum(image, roi_manager)
"""
+
+ rt_ = ResultsTable()
+ options = M.INTEGRATED_DENSITY
+ an = Analyzer (imp, options, rt_)
+ an.setPrecision(0)
+
label_id = []
sum_intensity = []
- target_img = ImageJFunctions.wrap(target_imp) # convert ImagePlus to img to use ops/region measurements on it
- regions = convert_labelimage_to_imglib2regions(label_imp)
-
- for region in regions:
- label_id.append(region.getLabel() + 1) # region.getlabel() starts counting from 0. So the label with int 1 has the index 0.
- input = Regions.sample(region, target_img) # returns an iterableInterval
- sum = ops.stats().sum(input).getRealDouble()
- sum_intensity.append(sum)
- # other measurements see https://forum.image.sc/t/can-i-get-to-measurements-using-imagej-ops/4448/5
- result = [label_id, sum_intensity]
+
+ for index, roi in enumerate(rm.getRoisAsArray()):
+ imp.setRoi(roi)
+ an.measure()
+ label_id.append(roi.getName())
+ sum_intensity.append(int(rt_.getColumn("RawIntDen")[index]))
- return result
+ return label_id, sum_intensity
def add_results_to_resultstable(results_table, column, values):
--
GitLab
From b0af87596a1e8f182c347914c8c1e19afeb46d60 Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Wed, 16 Apr 2025 10:15:16 +0200
Subject: [PATCH 20/26] Remove unused function and imports
---
2d_spots_in_fibers.py | 31 -------------------------------
1 file changed, 31 deletions(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index 181b435..f6ec4ba 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -29,11 +29,6 @@ from loci.plugins.in import ImporterOptions
from loci.formats import ImageReader, MetadataTools, Memoizer
# MorpholibJ imports
from inra.ijpb.binary import BinaryImages
-# imglib2 imports
-from net.imglib2.img.display.imagej import ImageJFunctions
-from net.imglib2.roi import Regions
-from net.imglib2.roi.labeling import LabelRegions
-from net.imglib2.algorithm.labeling import ConnectedComponents
# BIOP imports
from ch.epfl.biop.ij2command import Labels2Rois, Rois2Labels
# python imports
@@ -288,32 +283,6 @@ def save_image_as_IJtif(imp, filename, suffix, target):
IJ.saveAs(imp, "Tiff", savepath)
-def convert_labelimage_to_imglib2regions(imp):
- """Convert a ImagePlus label image to imglib2 regions
-
- Parameters
- ----------
- imp : ImagePlus
- the input label image
-
- Returns
- -------
- Imglib2 LabelRegions
- the imglib2 label regions
- """
-
- # fist convert ImagePlus to img as suggested by curtis:
- # from https://forum.image.sc/t/how-to-wrap-any-kind-of-imageplus-to-an-imglib2-img-floattype/178/6
- wrapImg = ImageJFunctions.wrap(imp)
- # workaround to convert a label image into an imglib2 ImgLabeling (which contains not only an image)
- img_labeling = ops.labeling().cca(wrapImg, ConnectedComponents.StructuringElement.EIGHT_CONNECTED)
- # img = img_labeling.getIndexImg() # the img label image
- # ImageJFunctions.show(img)
- regions = LabelRegions(img_labeling)
-
- return regions
-
-
def convert_labelimage_to_binary(label_imp, scale_binary=True):
"""Convert a label image to a mask / binary image
--
GitLab
From 06b45e9a216aaa06f37922d108ed7472d91043eb Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Wed, 16 Apr 2025 10:18:03 +0200
Subject: [PATCH 21/26] Adapt to new function
---
2d_spots_in_fibers.py | 14 +++++++-------
1 file changed, 7 insertions(+), 7 deletions(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index f6ec4ba..0cca227 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -486,15 +486,15 @@ for index, channel in enumerate(processing_channels):
dapi_positive_spots_binary = ImageCalculator.run(spots_binary_imp, dapi_binary, "Multiply create")
dapi_negative_spots_binary = ImageCalculator.run(spots_binary_imp, dapi_positive_spots_binary, "Subtract create")
- n_spots_per_fiber = measure_intensity_sum(fibers_label_imp, spots_binary_imp)
- n_dapi_positive_spots_per_fiber = measure_intensity_sum(fibers_label_imp, dapi_positive_spots_binary)
- n_dapi_negative_spots_per_fiber = measure_intensity_sum(fibers_label_imp, dapi_negative_spots_binary)
+ fiber_label_IDs, n_spots_per_fiber = measure_intensity_sum(fibers_label_imp, spots_binary_imp)
+ _, n_dapi_positive_spots_per_fiber = measure_intensity_sum(fibers_label_imp, dapi_positive_spots_binary)
+ _, n_dapi_negative_spots_per_fiber = measure_intensity_sum(fibers_label_imp, dapi_negative_spots_binary)
# TODO: the column fiber label ID needs to be added only one time. Maybe check before if column exists.
- add_results_to_resultstable(results_table, "fiber label ID", n_spots_per_fiber[0])
- add_results_to_resultstable(results_table, "n spots channel " + str(channel), n_spots_per_fiber[1])
- add_results_to_resultstable(results_table, "n spots dapi positive channel " + str(channel), n_dapi_positive_spots_per_fiber[1])
- add_results_to_resultstable(results_table, "n spots dapi negative channel " + str(channel), n_dapi_negative_spots_per_fiber[1])
+ add_results_to_resultstable(results_table, "fiber label ID", fiber_label_IDs)
+ add_results_to_resultstable(results_table, "n spots channel " + str(channel), n_spots_per_fiber)
+ add_results_to_resultstable(results_table, "n spots dapi positive channel " + str(channel), n_dapi_positive_spots_per_fiber)
+ add_results_to_resultstable(results_table, "n spots dapi negative channel " + str(channel), n_dapi_negative_spots_per_fiber)
close_images([spots_channel, spots_label_imp, spots_binary_imp, spots_binary_imp, dapi_binary, dapi_positive_spots_binary, dapi_negative_spots_binary])
results_table.show("Spots")
--
GitLab
From f1bac837022bba94df110cae398bfd95e10678ce Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Wed, 16 Apr 2025 10:18:03 +0200
Subject: [PATCH 22/26] Adapt to new function
---
2d_spots_in_fibers.py | 17 +++++++++--------
1 file changed, 9 insertions(+), 8 deletions(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index f6ec4ba..3924854 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -485,16 +485,17 @@ for index, channel in enumerate(processing_channels):
spots_binary_imp = convert_labelimage_to_binary(spots_label_imp)
dapi_positive_spots_binary = ImageCalculator.run(spots_binary_imp, dapi_binary, "Multiply create")
dapi_negative_spots_binary = ImageCalculator.run(spots_binary_imp, dapi_positive_spots_binary, "Subtract create")
-
- n_spots_per_fiber = measure_intensity_sum(fibers_label_imp, spots_binary_imp)
- n_dapi_positive_spots_per_fiber = measure_intensity_sum(fibers_label_imp, dapi_positive_spots_binary)
- n_dapi_negative_spots_per_fiber = measure_intensity_sum(fibers_label_imp, dapi_negative_spots_binary)
+
+ load_rois_from_zip(fiber_segmentation_roiset)
+ fiber_label_IDs, n_spots_per_fiber = measure_intensity_sum(spots_binary_imp, rm)
+ _, n_dapi_positive_spots_per_fiber = measure_intensity_sum(dapi_positive_spots_binary, rm)
+ _, n_dapi_negative_spots_per_fiber = measure_intensity_sum(dapi_negative_spots_binary, rm)
# TODO: the column fiber label ID needs to be added only one time. Maybe check before if column exists.
- add_results_to_resultstable(results_table, "fiber label ID", n_spots_per_fiber[0])
- add_results_to_resultstable(results_table, "n spots channel " + str(channel), n_spots_per_fiber[1])
- add_results_to_resultstable(results_table, "n spots dapi positive channel " + str(channel), n_dapi_positive_spots_per_fiber[1])
- add_results_to_resultstable(results_table, "n spots dapi negative channel " + str(channel), n_dapi_negative_spots_per_fiber[1])
+ add_results_to_resultstable(results_table, "fiber label ID", fiber_label_IDs)
+ add_results_to_resultstable(results_table, "n spots channel " + str(channel), n_spots_per_fiber)
+ add_results_to_resultstable(results_table, "n spots dapi positive channel " + str(channel), n_dapi_positive_spots_per_fiber)
+ add_results_to_resultstable(results_table, "n spots dapi negative channel " + str(channel), n_dapi_negative_spots_per_fiber)
close_images([spots_channel, spots_label_imp, spots_binary_imp, spots_binary_imp, dapi_binary, dapi_positive_spots_binary, dapi_negative_spots_binary])
results_table.show("Spots")
--
GitLab
From d34dc6c34cd1314d43d0d965045cba0d5844e6cc Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Wed, 16 Apr 2025 11:54:35 +0200
Subject: [PATCH 23/26] Remove unused function, its execution and associated
import
---
2d_spots_in_fibers.py | 22 +++-------------------
1 file changed, 3 insertions(+), 19 deletions(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index 3924854..22b3a45 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -30,7 +30,7 @@ from loci.formats import ImageReader, MetadataTools, Memoizer
# MorpholibJ imports
from inra.ijpb.binary import BinaryImages
# BIOP imports
-from ch.epfl.biop.ij2command import Labels2Rois, Rois2Labels
+from ch.epfl.biop.ij2command import Labels2Rois
# python imports
import os
@@ -330,7 +330,7 @@ def measure_intensity_sum(imp, rm):
Example
-------
- >>> labels, intensities = measure_intensity_sum(image, roi_manager)
+ >>> labels, intensities = measure_intensity_sum(imp, roi_manager)
"""
rt_ = ResultsTable()
@@ -428,17 +428,6 @@ def load_rois_from_zip(path):
rm.runCommand("Open", path)
-def convert_rois_to_labelimage(imp):
- rm = RoiManager.getInstance()
- if not rm:
- rm = RoiManager()
-
- label_imp = command.run( Rois2Labels , False , 'imp' , imp , 'rm', rm).get().getOutput("label_imp")
- rm.reset() # TODO: should be optional but can be default
-
- return label_imp
-
-
def close_images(list_of_imps):
"""Close given ImagePlus images
@@ -468,11 +457,6 @@ if threshold <= 0:
threshold = get_threshold_from_method(dapi_channel, "otsu")
dapi_binary = convert_to_binary(dapi_channel, threshold)
-# Get the fiber segmentation from ij roizip and convert to labelimage
-load_rois_from_zip(fiber_segmentation_roiset)
-fibers_label_imp = convert_rois_to_labelimage(dapi_channel)
-dapi_channel.close()
-
# detect spots and count them per fiber
results_table = ResultsTable()
for index, channel in enumerate(processing_channels):
@@ -480,7 +464,7 @@ for index, channel in enumerate(processing_channels):
quality_threshold = float(quality_thresholds[index])
spots_channel = BFopen_image(path_to_image, channel, series_number)
spots_label_imp = run_trackmate_dog_spot_detector(spots_channel, spot_diameter, quality_threshold)
- save_image_as_IJtif(spots_label_imp, filename, "spots_ch" + str(channel), parent_dir)
+ # save_image_as_IJtif(spots_label_imp, filename, "spots_ch" + str(channel), parent_dir)
save_labelimage_as_ijroiset(spots_label_imp, filename, "spots_ch" + str(channel), parent_dir)
spots_binary_imp = convert_labelimage_to_binary(spots_label_imp)
dapi_positive_spots_binary = ImageCalculator.run(spots_binary_imp, dapi_binary, "Multiply create")
--
GitLab
From 2c6afe8e3b650fa6903587504ae828841bc3b99b Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Wed, 16 Apr 2025 13:32:55 +0200
Subject: [PATCH 24/26] Remove RoiManager import, get from script parameter
instead.
---
2d_spots_in_fibers.py | 16 ++++------------
1 file changed, 4 insertions(+), 12 deletions(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index 22b3a45..acf308f 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -18,7 +18,6 @@ from fiji.plugin.trackmate.action import LabelImgExporter
# ij imports
from ij import IJ
from ij.plugin import ImageCalculator
-from ij.plugin.frame import RoiManager
from ij.measure import ResultsTable
from ij.measure import Measurements as M
from ij.plugin.filter import Analyzer
@@ -386,7 +385,7 @@ def save_results_table(results_table, filename, suffix, target):
results_table.save(savepath)
-def save_labelimage_as_ijroiset(label_imp, filename, suffix, target):
+def save_labelimage_as_ijroiset(label_imp, rm, filename, suffix, target):
"""Save all labels i a label Images as IJ-ROIset to target location.
Only 2D, requires PTBIOP update site.
@@ -401,10 +400,6 @@ def save_labelimage_as_ijroiset(label_imp, filename, suffix, target):
target : str
the target directory in which to save the table
"""
- rm = RoiManager.getInstance()
- if not rm:
- rm = RoiManager()
- rm.reset()
command.run( Labels2Rois , False , 'imp' , label_imp , 'rm', rm).get()
savename = filename + "_" + str(suffix) + ".zip"
savepath = os.path.join(target, savename)
@@ -412,19 +407,16 @@ def save_labelimage_as_ijroiset(label_imp, filename, suffix, target):
rm.reset()
-def load_rois_from_zip(path):
+def load_rois_from_zip(path, rm):
"""Load ROIs from the given zip file and add them to the RoiManager.
Parameters
----------
path : string
Path to the ROI zip file.
+ rm : RoiManager
+ The ROI Manager.
"""
- rm = RoiManager.getInstance()
- if not rm:
- rm = RoiManager()
- rm.reset()
-
rm.runCommand("Open", path)
--
GitLab
From 1725ac7ff988c22b15dea5587afc6c222f76a795 Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Wed, 16 Apr 2025 13:37:31 +0200
Subject: [PATCH 25/26] Remove unused line
---
2d_spots_in_fibers.py | 1 -
1 file changed, 1 deletion(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index acf308f..34332f1 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -456,7 +456,6 @@ for index, channel in enumerate(processing_channels):
quality_threshold = float(quality_thresholds[index])
spots_channel = BFopen_image(path_to_image, channel, series_number)
spots_label_imp = run_trackmate_dog_spot_detector(spots_channel, spot_diameter, quality_threshold)
- # save_image_as_IJtif(spots_label_imp, filename, "spots_ch" + str(channel), parent_dir)
save_labelimage_as_ijroiset(spots_label_imp, filename, "spots_ch" + str(channel), parent_dir)
spots_binary_imp = convert_labelimage_to_binary(spots_label_imp)
dapi_positive_spots_binary = ImageCalculator.run(spots_binary_imp, dapi_binary, "Multiply create")
--
GitLab
From 5147222ec3466788869a32d38d066a417f6ac7a5 Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Wed, 16 Apr 2025 14:07:59 +0200
Subject: [PATCH 26/26] Pass RoiManager to functions
---
2d_spots_in_fibers.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index 34332f1..4e0a816 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -456,12 +456,12 @@ for index, channel in enumerate(processing_channels):
quality_threshold = float(quality_thresholds[index])
spots_channel = BFopen_image(path_to_image, channel, series_number)
spots_label_imp = run_trackmate_dog_spot_detector(spots_channel, spot_diameter, quality_threshold)
- save_labelimage_as_ijroiset(spots_label_imp, filename, "spots_ch" + str(channel), parent_dir)
+ save_labelimage_as_ijroiset(spots_label_imp, rm, filename, "spots_ch" + str(channel), parent_dir)
spots_binary_imp = convert_labelimage_to_binary(spots_label_imp)
dapi_positive_spots_binary = ImageCalculator.run(spots_binary_imp, dapi_binary, "Multiply create")
dapi_negative_spots_binary = ImageCalculator.run(spots_binary_imp, dapi_positive_spots_binary, "Subtract create")
- load_rois_from_zip(fiber_segmentation_roiset)
+ load_rois_from_zip(fiber_segmentation_roiset, rm)
fiber_label_IDs, n_spots_per_fiber = measure_intensity_sum(spots_binary_imp, rm)
_, n_dapi_positive_spots_per_fiber = measure_intensity_sum(dapi_positive_spots_binary, rm)
_, n_dapi_negative_spots_per_fiber = measure_intensity_sum(dapi_negative_spots_binary, rm)
--
GitLab