cellects 0.1.2__py3-none-any.whl → 0.2.6__py3-none-any.whl

cellects/gui/ui_strings.py

@@ -0,0 +1,840 @@
+#!/usr/bin/env python3
+
+########################################
+#########     First Window     #########
+########################################
+
+FW = dict()
+FW["Image_list_or_videos"] = {}
+FW["Image_list_or_videos"]["label"] = "Image list or videos"
+# START_TIP
+FW["Image_list_or_videos"]["tips"] = \
+f"""The *Image list or video* option indicates whether the data have been stored as an image stack (i.e.
+a set of files where each file contains a single image) or as a video. Images must be named
+alphanumerically so the program can read them in the right order.
+"""
+# END_TIP
+
+FW["Image_prefix_and_extension"] = {}
+FW["Image_prefix_and_extension"]["label"] = "Image prefix and extension"
+# START_TIP
+FW["Image_prefix_and_extension"]["tips"] = \
+f"""The *Images prefix* and *Images extension* fields allow Cellects to consider relevant data. For
+example, setting 'exp_' as image prefix and '.jpg' as image extension will cause Cellects to only
+consider JPG files whose name starts with 'exp_'. Remaining labels should indicate the order in
+which images were taken.
+NB:
+- Image prefix is optional
+- If every .jpg files start with IMG_ but other .jpg files exist, use the prefix to exclude
+irrelevant files.
+- Supported formats: bmp, dib, exr, exr, hdr, jp2, jpe, jpeg, jpg, pbm, pfm, pgm, pic, png,  pnm,
+ppm, ras, sr, tif, tiff, webp, cr2, cr3, nef, arw, sr2, raf, prf, rw2, pef, dng, 3fr, iiq.
+"""
+# END_TIP
+
+FW["Folder"] = {}
+FW["Folder"]["label"] = "Folder"
+# START_TIP
+FW["Folder"]["tips"] = \
+f"""The *Folder* field must specify the directory path to the folder(s) for Cellects to be able to run
+the analysis. The user can copy/paste this path into the field or navigate to the folder using the
+*Browse* push button. For batch analysis, provide a path leading directly to the parent folder
+containing all subfolders.
+"""
+# END_TIP
+
+FW["Arena_number_per_folder"] = {}
+FW["Arena_number_per_folder"]["label"] = "Arena number per folder"
+# START_TIP
+FW["Arena_number_per_folder"]["tips"] = \
+f"""The *Arena number per folder* specifies how many arenas are present in the images. Cellects will
+process and analyze each arena separately.
+NB:
+- For batch processing, assign different arena counts for each subfolder (see Fig. 11: the several
+folder window).
+"""
+# END_TIP
+
+FW["Browse"] = {}
+FW["Browse"]["label"] = "Browse"
+# START_TIP
+FW["Browse"]["tips"] = \
+f"""Clicking the *Browse* button opens a dialog to select a folder for analysis.
+"""
+# END_TIP
+
+FW["Required_outputs"] = {}
+FW["Required_outputs"]["label"] = "Required outputs"
+# START_TIP
+FW["Required_outputs"]["tips"] = \
+f"""Clicking the *Required outputs* button opens the window allowing to choose what descriptors Cellects
+will compute on the selected data. Find details about this window in the advanced documentation.
+"""
+# END_TIP
+
+FW["Advanced_parameters"] = {}
+FW["Advanced_parameters"]["label"] = "Advanced parameters"
+# START_TIP
+FW["Advanced_parameters"]["tips"] = \
+f"""Clicking the *Advanced parameters* button opens the window containing all secondary parameters of
+the software.  Find details about this window in the advanced documentation.
+"""
+# END_TIP
+
+FW["Run_all_directly"] = {}
+FW["Run_all_directly"]["label"] = "Run all directly"
+# START_TIP
+FW["Run_all_directly"]["tips"] = \
+f"""This option appears when image analysis has already been performed for the current folder. It is a
+shortcut to bypass the image analysis step and proceed directly to video tracking refinement.
+"""
+# END_TIP
+
+FW["Next"] = {}
+FW["Next"]["label"] = "Next"
+# START_TIP
+FW["Next"]["tips"] = \
+f"""Click the *Next* button to go to the image analysis window (Fig. 2), or  to the window showing the
+list of folders (Fig. 11) if applicable.
+"""
+# END_TIP
+
+#######################################
+######### ImageAnalysisWindow #########
+#######################################
+
+IAW = dict()
+IAW["Image_number"] = {}
+IAW["Image_number"]["label"] = "Image number"
+# START_TIP
+IAW["Image_number"]["tips"] = \
+f"""Selects the image number to analyze. This number should only be changed when specimen(s) are
+invisible on the first image (e.g., in the case of appearing colonies of bacteria), never otherwise.
+When the specimen(s) are invisible, read more advanced images until some material can be detected.
+NB:
+- When the data is stored as images, this image number comes from alphanumerical sorting of original
+image labels.
+"""
+# END_TIP
+
+IAW["several_blob_per_arena"] = {}
+IAW["several_blob_per_arena"]["label"] = "One specimen per arena"
+# START_TIP
+IAW["several_blob_per_arena"]["tips"] = \
+f"""Select this option if there is only one specimen (e.g., a cell or connected colony) per arena. If
+multiple specimens exist (or will be present) in an arena, unselect this option.
+NB:
+- This option is selected by default.
+"""
+# END_TIP
+
+IAW["Scale_with"] = {}
+IAW["Scale_with"]["label"] = "Scale with"
+# START_TIP
+IAW["Scale_with"]["tips"] = \
+f"""Specify how to compute true pixel size (in mm). Cellects can determine this scale using:
+- Image width (horizontal dimension)
+- Specimen width on first image (usable when specimens share consistent width)
+NB:
+- Advanced parameters allow disabling scaling and outputting in pixels.
+- Using specimen width reduces initial detection efficiency. We recommend using image width unless
+specimen dimensions are known with higher accuracy than imaging equipment.
+- Pixel size is stored in a file named `software_settings.csv`.
+"""
+# END_TIP
+
+IAW["Scale_size"] = {}
+IAW["Scale_size"]["label"] = "Scale size"
+# START_TIP
+IAW["Scale_size"]["tips"] = \
+f"""The *Scale size* is the actual length (in mm) corresponding to scaling reference.
+NB:
+- This value enables conversion from pixel coordinates to physical dimensions.
+"""
+# END_TIP
+
+IAW["Select_and_draw"] = {}
+IAW["Select_and_draw"]["label"] = "Select and draw"
+# START_TIP
+IAW["Select_and_draw"]["tips"] = \
+f"""*Select and draw* allows the user to inform Cellects about specimen (*Cell*) and background (*Back*)
+areas in images. To use, click *Cell* or *Back* button (button color changes), then:
+- Click and drag mouse on image to mark corresponding area
+- Numbered drawings appear below buttons for reference
+- (if needed) Click numbered drawing to remove selection.
+NB:
+- By default, this tool only works for the first folder when analyzing multiple folders. Advanced
+parameters include an option to use these same masks in multiple folders.
+- To apply saved masks (e.g., background or specimen initiation regions) across selected folders,
+enable *Keep Cell and Back drawing for all folders* in *Advanced parameters*.
+"""
+# END_TIP
+
+IAW["Draw_buttons"] = {}
+IAW["Draw_buttons"]["label"] = "Draw buttons"
+# START_TIP
+IAW["Draw_buttons"]["tips"] = \
+f"""Click the *Cell* or *Back* button and draw a corresponding area on the image by clicking and holding
+mouse on the image.
+"""
+# END_TIP
+
+IAW["Advanced_mode"] = {}
+IAW["Advanced_mode"]["label"] = "Advanced mode"
+# START_TIP
+IAW["Advanced_mode"]["tips"] = \
+f"""The *Advanced mode* enables fine tuning of image analysis parameters for:
+- Custom color space combinations (e.g., HSV, HLS)
+- Applying filters before segmentation
+- Combining segmentations using logical operators
+- Accessing rolling window and Kmeans algorithms
+NB:
+- Useful for reusing validated parameter sets or testing alternative methods.
+"""
+# END_TIP
+
+IAW["Color_combination"] = {}
+IAW["Color_combination"]["label"] = "Color combination"
+# START_TIP
+IAW["Color_combination"]["tips"] = \
+f"""Color spaces are transformations of the original BGR (Blue Green Red) image Instead of defining an
+image by 3 colors,  they transform it into 3 different visual properties
+- hsv: hue (color), saturation, value (lightness)
+- hls: hue (color), lightness, saturation
+- lab: Lightness, Red/Green, Blue/Yellow
+- luv and yuv: l and y are Lightness, u and v are related to colors
+"""
+# END_TIP
+
+IAW["Logical_operator"] = {}
+IAW["Logical_operator"]["label"] = "Logical operator"
+# START_TIP
+IAW["Logical_operator"]["tips"] = \
+f"""The *Logical operator* defines how to combine results from distinct segmentations (e.g., merging the
+segmentation resulting from a specific color space transformation and filtering with a different
+one). Supported operators: AND, OR, XOR.
+"""
+# END_TIP
+
+IAW["Filter"] = {}
+IAW["Filter"]["label"] = "Filter"
+# START_TIP
+IAW["Filter"]["tips"] = \
+f"""Apply a filter to preprocess images before segmentation.
+NB:
+- Filtering can improve segmentation accuracy by emphasizing relevant image features.
+"""
+# END_TIP
+
+IAW["Rolling_window_segmentation"] = {}
+IAW["Rolling_window_segmentation"]["label"] = "Rolling window segmentation"
+# START_TIP
+IAW["Rolling_window_segmentation"]["tips"] = \
+f"""Segments image regions using a rolling window approach to detect local intensity valleys. The method
+applies Otsu's thresholding locally on each window.
+"""
+# END_TIP
+
+IAW["Kmeans"] = {}
+IAW["Kmeans"]["label"] = "Kmeans"
+# START_TIP
+IAW["Kmeans"]["tips"] = \
+f"""The *Kmeans* algorithm clusters pixels into a specified number of categories (2
+-5) to identify specimen regions within the image.
+"""
+# END_TIP
+
+IAW["Generate_analysis_options"] = {}
+IAW["Generate_analysis_options"]["label"] = "Generate analysis options"
+# START_TIP
+IAW["Generate_analysis_options"]["tips"] = \
+f"""Cellects proposes algorithms to automatically determine optimal specimen detection parameters on the
+first or last image:
+- **Basic** → provides suggestions in minutes. Alternatively, the user can switch to *Advanced mode*
+to review or modify more specific settings.
+NB:
+- Selecting *Basic* (or *Apply current config*) will trigger an orange working message during
+processing.
+"""
+# END_TIP
+
+IAW["Select_option_to_read"] = {}
+IAW["Select_option_to_read"]["label"] = "Select option to read"
+# START_TIP
+IAW["Select_option_to_read"]["tips"] = \
+f"""Choose the option producing optimal segmentation results. This menu appears after generating
+analysis options, allowing direct quality assessment. For example, if Option 1 shows correct
+detection (e.g., 6 spots in 6 arenas), click *Yes*. Otherwise, improve analysis via:
+- Adjusting arena/spot shapes or sizes
+- Using *Select and draw* to annotate specimens/background
+- Manual configuration in advanced mode → Test changes with *Apply current config*
+NB:
+- Confirm when magenta/pink contours match expected positions and counts.
+"""
+# END_TIP
+
+IAW["Arena_shape"] = {}
+IAW["Arena_shape"]["label"] = "Arena shape"
+# START_TIP
+IAW["Arena_shape"]["tips"] = \
+f"""Specifies whether the specimen(s) can move in a circular or rectangular arena.
+"""
+# END_TIP
+
+IAW["Spot_shape"] = {}
+IAW["Spot_shape"]["label"] = "Set spot shape"
+# START_TIP
+IAW["Spot_shape"]["tips"] = \
+f"""Defines the expected shape of specimens within arenas.
+"""
+# END_TIP
+
+IAW["Spot_size"] = {}
+IAW["Spot_size"]["label"] = "Set spot size"
+# START_TIP
+IAW["Spot_size"]["tips"] = \
+f"""Initial horizontal size of the specimen(s) (in mm). If similar across all specimens, this can also
+be used as a scale.
+"""
+# END_TIP
+
+IAW["Video_delimitation"] = {}
+IAW["Video_delimitation"]["label"] = "Video delimitation"
+# START_TIP
+IAW["Video_delimitation"]["tips"] = \
+f"""After confirming initial detection, automatic video delimitation results appear in blue.  Click
+*Yes* if accurate or *No* for:
+- A slower, higher precision algorithm.
+- Manual delineation option.
+"""
+# END_TIP
+
+IAW["Last_image_question"] = {}
+IAW["Last_image_question"]["label"] = "Last image question"
+# START_TIP
+IAW["Last_image_question"]["tips"] = \
+f"""If parameters might fail on later images, test them first on the final frame:
+- *Yes* → validates with last image before tracking.
+- *No* → proceeds directly to video analysis.
+"""
+# END_TIP
+
+IAW["Start_differs_from_arena"] = {}
+IAW["Start_differs_from_arena"]["label"] = "Check if the medium at starting position differs from the rest of the arena"
+# START_TIP
+IAW["Start_differs_from_arena"]["tips"] = \
+f"""Enable if the substrate differs between initial position and arena growth area (e.g., nutritive gel
+vs. agar). Disable for homogeneous substrates.
+"""
+# END_TIP
+
+IAW["Save_image_analysis"] = {}
+IAW["Save_image_analysis"]["label"] = "Save image analysis"
+# START_TIP
+IAW["Save_image_analysis"]["tips"] = \
+f"""Complete the analysis of the current image. Clicking this button analyzes only one image. To analyze
+video(s), click *Next*.
+NB:
+- When analyzing a single specimen per arena, keeps the largest connected component.
+- Saves all selected descriptors in .csv format for the current image and generates a validation
+image to assess segmentation accuracy.
+"""
+# END_TIP
+
+
+#################################################
+#########     Video analysis Window     #########
+#################################################
+
+VAW = dict()
+VAW["Arena_to_analyze"] = {}
+VAW["Arena_to_analyze"]["label"] = "Arena to analyze"
+# START_TIP
+VAW["Arena_to_analyze"]["tips"] = \
+f"""This arena number selects a specific arena in the current folder. The user can choose an arena,
+click *Detection* to load and analyze it, then *Read* results.
+NB:
+- Cellects automatically names the arena by their position (left to right, top to bottom).
+- For single arena setups, use 1.
+- *Post processing* triggers *Detection*, which in turn triggers *Load One arena*.
+- Videos can be saved (as .npy files) for later analysis using the Advanced parameter *Keep
+unaltered videos*.
+"""
+# END_TIP
+
+VAW["Maximal_growth_factor"] = {}
+VAW["Maximal_growth_factor"]["label"] = "Maximal growth factor"
+# START_TIP
+VAW["Maximal_growth_factor"]["tips"] = \
+f"""This is the maximum allowable proportion of image area that may be covered by specimen movement
+between frames. Adjust accordingly:
+- Increase if specimen size is underestimated.
+- Decrease if specimen size is overestimated.
+NB:
+- Precisely, this defines an upper bound on relative coverage changes between sequential images.
+"""
+# END_TIP
+
+VAW["Temporal_smoothing"] = {}
+VAW["Temporal_smoothing"]["label"] = "Temporal smoothing"
+# START_TIP
+VAW["Temporal_smoothing"]["tips"] = \
+f"""Applies temporal smoothing to reduce noise and highlight long
+-term trends by averaging pixel intensity changes. Use when analyzing slope
+-based segmentation results.
+NB:
+- This uses a moving window algorithm on pixel intensity curves over time.
+- Excessive iterations produce constant values, preventing accurate detection.
+"""
+# END_TIP
+
+VAW["Segmentation_method"] = {}
+VAW["Segmentation_method"]["label"] = "Segmentation method"
+# START_TIP
+VAW["Segmentation_method"]["tips"] = \
+f"""Cellects includes five video tracking options:
+- **Frame option**: Applies the image analysis algorithm frame by frame, without temporal dynamics.
+- **Threshold option**: Compares pixel intensity with the average intensity of the whole image at
+each time step.
+- **Slope option**: Compares pixel intensity slopes with an automatically defined threshold.
+- **T and S option**: logical AND of threshold and slope options.
+- **T or S option**: logical OR of threshold and slope options.
+NB:
+- Selecting the *Compute all options* before dunning *Detection* allows method comparison.  Once
+analysis completes. Once the analysis completed, select one option and click *Read*.
+- Computing only one option is faster and requires less memory.
+- When *Heterogeneous background* or *Grid segmentation* has been selected in the image analysis
+window, only the *Frame* option remains available.
+"""
+# END_TIP
+
+VAW["Load_one_arena"] = {}
+VAW["Load_one_arena"]["label"] = "Load one arena"
+# START_TIP
+VAW["Load_one_arena"]["tips"] = \
+f"""Clicking this button loads the arena associated with *Arena to analyze*. The center of the window
+displays the first frame of that arena's video. Click *Read* to review the full video.
+"""
+# END_TIP
+
+VAW["Detection"] = {}
+VAW["Detection"]["label"] = "Detection"
+# START_TIP
+VAW["Detection"]["tips"] = \
+f"""*Detection* applies a (or all) segmentation methods to one arena. Once finished, click *Read*  to
+view the detection result. If correct, answer *Done* to proceed with tuning parameters for post
+processing.
+"""
+# END_TIP
+
+VAW["Read"] = {}
+VAW["Read"]["label"] = "Read"
+# START_TIP
+VAW["Read"]["tips"] = \
+f"""Clicking *Read* starts the video display corresponding to the current state of the analysis.
+"""
+# END_TIP
+
+VAW["Fading_detection"] = {}
+VAW["Fading_detection"]["label"] = "Fading detection"
+# START_TIP
+VAW["Fading_detection"]["tips"] = \
+f"""*Fading detection* monitors when specimens leave previously occupied areas, useful for  moving
+organisms rather than static growth. Uncheck this option if not needed. Set a value  between minus
+one and one to control sensitivity:
+- Near minus one: Minimal false removal of specimen traces.
+- Near one: High risk of over
+-removal from all areas.
+"""
+# END_TIP
+
+VAW["Post_processing"] = {}
+VAW["Post_processing"]["label"] = "Post processing"
+# START_TIP
+VAW["Post_processing"]["tips"] = \
+f"""*Post processing* applies detection algorithms with additional enhancements:
+- Binary operations: opening, closing, logical ops.
+- Fading detection* tracking: when specimen(s) may leave areas (optional).
+- *Correct errors around initial shape*: when the contour of the initial position of the specimen is
+hard to detect (optional).
+- *Connect distant shapes*: when the specimen's heterogeneity create wrong disconnections in the
+video detection (optional).
+- *Prevent fast growth near periphery*: when arena's border (typically petri dishes) may be wrongly
+detected as specimen (optional).
+NB:
+- Once Post processing works, the user can click “*Done*” to *Step 2: Tune fading and advanced
+parameters to improve Post processing*, and then *Run All* arenas.
+"""
+# END_TIP
+
+VAW["Save_one_result"] = {}
+VAW["Save_one_result"]["label"] = "Save one result"
+# START_TIP
+VAW["Save_one_result"]["tips"] = \
+f"""Complete the current video analysis by clicking this button for single arena processing. Saving
+includes:
+- Calculating all selected descriptors (.csv) per frame.
+- Generating validation videos for detection verification.
+- Storing configuration parameters for reproducibility.
+NB:
+- This action will overwrite results and validation data for the current arena.
+"""
+# END_TIP
+
+VAW["Run_All"] = {}
+VAW["Run_All"]["label"] = "Run All"
+# START_TIP
+VAW["Run_All"]["tips"] = \
+f"""Apply validated parameters to all arenas by clicking *Run All*. This action:
+- Generates full
+-resolution video outputs (storage
+-intensive)
+- Processes videos sequentially with real time visualization
+- Calculates selected descriptors for each frame
+- Produces validation content at multiple intervals
+- Preserves current configuration settings
+"""
+# END_TIP
+
+VAW["Save_all_choices"] = {}
+VAW["Save_all_choices"]["label"] = "Save all choices"
+# START_TIP
+VAW["Save_all_choices"]["tips"] = \
+f"""Clicking *Save all choices* writes/updates configuration files to preserve analysis parameters for
+future replication.
+"""
+# END_TIP
+
+#################################################
+########     Multiple folders Window     ########
+#################################################
+
+MF = dict()
+MF["Check_to_select_all_folders"] = {}
+MF["Check_to_select_all_folders"]["label"] = "Check to select all folders"
+# START_TIP
+MF["Check_to_select_all_folders"]["tips"] = \
+f"""Select this option to run the analysis on all folders containing images matching the *Image prefix*
+and *Images extension*. Otherwise, use Ctrl/Cmd to select specific folders for analysis.
+NB:
+- This setting affects only the *Run All* functionality.
+- To apply saved masks (e.g., background or specimen initiation regions) across selected folders,
+enable    *Keep Cell and Back drawing for all folders* in *Advanced parameters*.
+"""
+# END_TIP
+
+#################################################
+########     Required Output Window     ########
+#################################################
+
+RO = dict()
+RO["coord_specimen"] = {}
+RO["coord_specimen"]["label"] = "Pixels covered by the specimen(s)"
+# START_TIP
+RO["coord_specimen"]["tips"] = \
+f"""Save a .npy file containing coordinates (t, y, x) of specimen pixel presence as detected by current
+parameters.
+NB:
+- These files may consume significant memory depending on the total frame count.
+"""
+# END_TIP
+
+RO["Graph"] = {}
+RO["Graph"]["label"] = "Graph of the specimen(s) (or network)"
+# START_TIP
+RO["Graph"]["tips"] = \
+f"""Compute a geometrical graph describing the specimen based on current detection parameters.  Cellects
+generates this graph using the skeleton of the largest connected component per frame.  If network
+detection is enabled, it will be computed on the detected network instead. The output includes:
+- A .csv file for vertices with coordinates (t, y, x), IDs, tip status, part of the specimen's
+initial position, connection status with other vertices.
+- A .csv file for edges with IDs, vertex pairs, lengths, average width, and intensity.
+NB:
+- These files may consume significant memory depending on the total frame count.
+- Network and graph detection together are relevant only for organisms with a distinct internal
+network (e.g., *Physarum polycephalum*).
+"""
+# END_TIP
+
+RO["coord_oscillating"] = {}
+RO["coord_oscillating"]["label"] = "Oscillating areas in the specimen(s)"
+# START_TIP
+RO["coord_oscillating"]["tips"] = \
+f"""Compute and save (as .npy files) coordinates (t, y, x) of oscillating areas in the specimen(s).  Two
+files are generated: one for thickening regions and one for slimming regions.
+"""
+# END_TIP
+
+RO["coord_network"] = {}
+RO["coord_network"]["label"] = "Network in the specimen(s)"
+# START_TIP
+RO["coord_network"]["tips"] = \
+f"""Detect and save (as .npy file) coordinates (t, y, x) of a distinct network within the specimen(s).
+specimen(s).
+"""
+# END_TIP
+
+####################################################
+########     Advanced Parameters Window     ########
+####################################################
+
+AP = dict()
+AP["Crop_images"] = {}
+AP["Crop_images"]["label"] = "Automatically crop images"
+# START_TIP
+AP["Crop_images"]["tips"] = \
+f"""Uses initial image detection to crop all images and improve arena/last image detection.
+NB:
+- Unselect this option if analysis fails or crashes during image analysis.
+"""
+# END_TIP
+
+AP["Subtract_background"] = {}
+AP["Subtract_background"]["label"] = "Subtract background"
+# START_TIP
+AP["Subtract_background"]["tips"] = \
+f"""Takes the first image and subtracts it from subsequent images. This can improve or degrade detection
+depending on dataset characteristics.
+"""
+# END_TIP
+
+AP["Keep_drawings"] = {}
+AP["Keep_drawings"]["label"] = "Keep Cell and Back drawings for all folders"
+# START_TIP
+AP["Keep_drawings"]["tips"] = \
+f"""During initial image analysis, if the user drew cell/back regions to assist detection, this option
+saves and uses these annotations across all folders. In summary:
+- **Checked** → retain annotations for all folders
+- **Unchecked** → apply only to current folder
+"""
+# END_TIP
+
+AP["Correct_errors_around_initial"] = {}
+AP["Correct_errors_around_initial"]["label"] = "Correct errors around initial specimen's position"
+# START_TIP
+AP["Correct_errors_around_initial"]["tips"] = \
+f"""Applies an algorithm to correct detection errors near the initial specimen position due to color
+variations (e.g., from nutrient patches). Technical workflow:
+- Identifies potential gaps around initial position
+- Monitors local growth velocity
+- Fills gaps using growth patterns from adjacent pixels
+NB:
+- ⚠️ Not recommended if the substrate has the same transparency everywhere (i.e. no difference
+between starting and growth regions).
+"""
+# END_TIP
+
+AP["Prevent_fast_growth_near_periphery"] = {}
+AP["Prevent_fast_growth_near_periphery"]["label"] = "Prevent fast growth near periphery"
+# START_TIP
+AP["Prevent_fast_growth_near_periphery"]["tips"] = \
+f"""During video analysis, prevents false specimen detection at arena borders by filtering rapid
+periphery growth.
+- **Checked** → Exclude fast
+-moving detections near boundaries
+- **Unchecked** → Use standard detection criteria
+"""
+# END_TIP
+
+AP["Connect_distant_shapes"] = {}
+AP["Connect_distant_shapes"]["label"] = "Connect distant shapes"
+# START_TIP
+AP["Connect_distant_shapes"]["tips"] = \
+f"""Algorithm for connecting disjoint specimen regions in cases where there should be only one connected
+specimen per arena.  This is useful when the specimen's heterogeneity create wrong disconnections
+and the detection is smaller than the true specimen. Technical implementation:
+- Identifies disconnected subregions
+- Analyzes local growth dynamics
+- Recreates connections using spatially consistent growth patterns
+NB:
+- Increases analysis time substantially.
+"""
+# END_TIP
+
+AP["Specimens_have_same_direction"] = {}
+AP["Specimens_have_same_direction"]["label"] = "All specimens have the same direction"
+# START_TIP
+AP["Specimens_have_same_direction"]["tips"] = \
+f"""Select to optimize arena detection for specimens moving move in the same direction.
+- **Checked** → Uses motion pattern analysis for arena localization.
+- **Unchecked** → Employs standard centroid
+-based algorithm.
+"""
+# END_TIP
+
+AP["Appearance_size_threshold"] = {}
+AP["Appearance_size_threshold"]["label"] = "Appearance size threshold (automatic if checked)"
+# START_TIP
+AP["Appearance_size_threshold"]["tips"] = \
+f"""Minimum pixel count threshold for identifying specimen emergence (e.g., bacterial colony formation).
+- **Checked** → Automatic threshold calculation.
+- **Unchecked** → Manual user
+-defined threshold.
+"""
+# END_TIP
+
+AP["Appearance_detection_method"] = {}
+AP["Appearance_detection_method"]["label"] = "Appearance detection method"
+# START_TIP
+AP["Appearance_detection_method"]["tips"] = \
+f"""Selection criteria for initial specimen detection:
+- Largest: Based on component size metric.
+- Most central: Based on arena center proximity.
+NB:
+- Applicable only to progressively emerging specimens.
+"""
+# END_TIP
+
+AP["Mesh_side_length"] = {}
+AP["Mesh_side_length"]["label"] = "Mesh side length"
+# START_TIP
+AP["Mesh_side_length"]["tips"] = \
+f"""Pixel dimension for analysis window size.
+NB:
+- Must not exceed minimum image dimension
+"""
+# END_TIP
+
+AP["Mesh_step_length"] = {}
+AP["Mesh_step_length"]["label"] = "Mesh step"
+# START_TIP
+AP["Mesh_step_length"]["tips"] = \
+f"""The size of the step (in pixels) between consecutive rolling window positions.
+NB:
+- Must not exceed the mesh side length to ensure full coverage of the image.
+"""
+# END_TIP
+
+AP["Mesh_minimal_intensity_variation"] = {}
+AP["Mesh_minimal_intensity_variation"]["label"] = "Mesh minimal intensity variation"
+# START_TIP
+AP["Mesh_minimal_intensity_variation"]["tips"] = \
+f"""The minimal variation in intensity to consider that a given window does contain the specimen(s).
+NB:
+- This threshold is an intensity value ranging from 0 to 255 (generally small).
+- Correspond to the level of noise in the background.
+"""
+# END_TIP
+
+AP["Expected_oscillation_period"] = {}
+AP["Expected_oscillation_period"]["label"] = "Expected oscillation period"
+# START_TIP
+AP["Expected_oscillation_period"]["tips"] = \
+f"""The period (in minutes) of biological oscillations to detect within the specimen(s). Computation is
+based on luminosity variations.
+"""
+# END_TIP
+
+AP["Minimal_oscillating_cluster_size"] = {}
+AP["Minimal_oscillating_cluster_size"]["label"] = "Minimal oscillating cluster size"
+# START_TIP
+AP["Minimal_oscillating_cluster_size"]["tips"] = \
+f"""When looking for oscillatory patterns, Cellects detects connected components that are thickening or
+slimming synchronously in the specimen(s). This parameter thresholds the minimal size of these
+groups of connected pixels. This threshold is useful to filter out small noisy oscillations.
+"""
+# END_TIP
+
+AP["Spatio_temporal_scaling"] = {}
+AP["Spatio_temporal_scaling"]["label"] = "Spatio-temporal scaling"
+# START_TIP
+AP["Spatio_temporal_scaling"]["tips"] = \
+f"""Defines the spatiotemporal scale of the dataset:
+- Time between images or frames (minutes).
+- An option to convert areas/distances from pixels to mm/mm².
+"""
+# END_TIP
+
+AP["Parallel_analysis"] = {}
+AP["Parallel_analysis"]["label"] = "Run analysis in parallel"
+# START_TIP
+AP["Parallel_analysis"]["tips"] = \
+f"""Allow the use of more than one core of the computer processor.
+- **Checked** → Uses multiple CPU cores to analyze arenas in parallel (faster).
+- **Unchecked** → Single core analysis.
+"""
+# END_TIP
+
+AP["Proc_max_core_nb"] = {}
+AP["Proc_max_core_nb"]["label"] = "Proc max core number"
+# START_TIP
+AP["Proc_max_core_nb"]["tips"] = \
+f"""Maximum number of logical CPU cores to use during analysis. The default value is set to the total
+number of available CPU cores minus one.
+"""
+# END_TIP
+
+AP["Minimal_RAM_let_free"] = {}
+AP["Minimal_RAM_let_free"]["label"] = "Minimal RAM let free"
+# START_TIP
+AP["Minimal_RAM_let_free"]["tips"] = \
+f"""Amount of RAM that should be left available for other programs. Setting to `0` gives Cellects all
+memory, but increases crash risk if other apps are open.
+"""
+# END_TIP
+
+AP["Lose_accuracy_to_save_RAM"] = {}
+AP["Lose_accuracy_to_save_RAM"]["label"] = "Lose accuracy to save RAM"
+# START_TIP
+AP["Lose_accuracy_to_save_RAM"]["tips"] = \
+f"""For low memory systems:
+- Converts video from `np.float64` to `uint8`
+- Saves RAM at the cost of a slight precision loss
+"""
+# END_TIP
+
+AP["Video_fps"] = {}
+AP["Video_fps"]["label"] = "Video fps"
+# START_TIP
+AP["Video_fps"]["tips"] = \
+f"""Frames per second of validation videos.
+"""
+# END_TIP
+
+AP["Keep_unaltered_videos"] = {}
+AP["Keep_unaltered_videos"]["label"] = 'Keep unaltered videos'
+# START_TIP
+AP["Keep_unaltered_videos"]["tips"] = \
+f"""Keeps unaltered `.npy` videos in hard drive.
+- **Checked** → Rerunning the same analysis will be faster.
+- **Unchecked** → These videos will be written and removed each run of the same analysis.
+NB:
+- Large files: it is recommended to remove them once analysis is entirely finalized.
+"""
+# END_TIP
+
+AP["Save_processed_videos"] = {}
+AP["Save_processed_videos"]["label"] = 'Save processed videos'
+# START_TIP
+AP["Save_processed_videos"]["tips"] = \
+f"""Saves lightweight processed validation videos (recommended over unaltered videos). These videos
+assess analysis accuracy and can be read in standard video players.
+"""
+# END_TIP
+
+AP["Csc_for_video_analysis"] = {}
+AP["Csc_for_video_analysis"]["label"] = 'Color space combination for video analysis'
+# START_TIP
+AP["Csc_for_video_analysis"]["tips"] = \
+f"""Advanced option: Changes the way RGB processing directly in video tracking. Useful for testing new
+color spaces without (re)running image analysis.
+"""
+# END_TIP
+
+AP["Night_mode"] = {}
+AP["Night_mode"]["label"] = 'Night mode'
+# START_TIP
+AP["Night_mode"]["tips"] = \
+f"""Switches the application background between light and dark themes.
+"""
+# END_TIP
+
+AP["Reset_all_settings"] = {}
+AP["Reset_all_settings"]["label"] = 'Reset all settings'
+# START_TIP
+AP["Reset_all_settings"]["tips"] = \
+f"""Useful when the software freezes with no apparent reason. To reset all settings, it removes the
+config file in the  current folder as well as the config file in the software folder. Then, it
+retrieves and saves the default parameters.
+"""
+# END_TIP