napari-tmidas 0.1.8__tar.gz → 0.1.9__tar.gz

{napari_tmidas-0.1.8 → napari_tmidas-0.1.9}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: napari-tmidas
-Version: 0.1.8
-Summary: Tissue Microscopy Image Data Analysis Suite
+Version: 0.1.9
+Summary: A plugin for batch processing of confocal and whole-slide microscopy images of biological tissues
 Author: Marco Meer
 Author-email: marco.meer@pm.me
 License: 
@@ -58,6 +58,14 @@ Requires-Dist: magicgui
 Requires-Dist: qtpy
 Requires-Dist: scikit-image
 Requires-Dist: pyqt5
+Requires-Dist: tqdm
+Requires-Dist: scikit-image
+Requires-Dist: ome-zarr
+Requires-Dist: napari-ome-zarr
+Requires-Dist: torch
+Requires-Dist: torchvision
+Requires-Dist: timm
+Requires-Dist: opencv-python
 Provides-Extra: testing
 Requires-Dist: tox; extra == "testing"
 Requires-Dist: pytest; extra == "testing"
@@ -75,34 +83,14 @@ Dynamic: license-file
 [![tests](https://github.com/macromeer/napari-tmidas/workflows/tests/badge.svg)](https://github.com/macromeer/napari-tmidas/actions)
 [![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-tmidas)](https://napari-hub.org/plugins/napari-tmidas)
 <!-- [![codecov](https://codecov.io/gh/macromeer/napari-tmidas/branch/main/graph/badge.svg)](https://codecov.io/gh/macromeer/napari-tmidas) -->
-The `napari-tmidas` plugin consists of a growing collection of pipelines for fast batch processing of microscopy images. This is a WIP and based on the CLI version of [T-MIDAS](https://github.com/MercaderLabAnatomy/T-MIDAS).
-
-## Feature Overview
-
-1. **Image Processing**
-   - Process image folders with: Gamma correction, Z-projection, channel splitting, Gaussian/median filters, thresholding (Otsu/manual), and label cleaning
-
-2. **Label Inspection**
-   - Review and edit label images with auto-save
-
-3. **Microscopy Image Conversion**
-   - Convert .nd2/.lif/.ndpi/.czi/acquifer → .tif/.zarr with metadata preservation
-
-4. **Crop Anything**
-   - Interactive ROI selection via click interface
-
-5. **ROI Colocalization**
-   - Count colocalized labels across multiple channels
-
-
-
-### Coming Soon
-New features arriving April 2025
+The `napari-tmidas` plugin consists of a growing collection of pipelines for fast batch processing of confocal and whole slide microscopy images of biological tissues. This is a WIP and based on the CLI version of [T-MIDAS](https://github.com/MercaderLabAnatomy/T-MIDAS).
 
+## Features
+Currently, napari-tmidas provides pipelines as widgets for batch image conversion / cropping / processing, ROI colocalization and label inspection (cf. [Usage](#usage) below).
 
 ## Installation
 
-First install Napari in a virtual environment:
+First, install Napari in a virtual environment:
 
     mamba create -y -n napari-tmidas -c conda-forge python=3.11 tqdm
     mamba activate napari-tmidas
@@ -112,19 +100,27 @@ Now you can install `napari-tmidas` via [pip]:
 
     pip install napari-tmidas
 
-To install the latest development version:
+It is recommended to install the latest development version:
 
     pip install git+https://github.com/macromeer/napari-tmidas.git
 
 ### Dependencies
-To use the Batch Microscopy Image Conversion pipeline, we need some libraries to read microscopy formats and to write ome-zarr:
 
-    pip install nd2 readlif tiffslide pylibCZIrw acquifer-napari ome-zarr napari-ome-zarr
+To use the Batch Microscopy Image Conversion pipeline, we need some libraries to read microscopy formats:
+
+    pip install nd2 readlif tiffslide pylibCZIrw acquifer-napari
 
 For the Batch Crop Anything pipeline, we need to install MobileSAM and its dependencies:
 
     pip install git+https://github.com/ChaoningZhang/MobileSAM.git
-    pip install torch torchvision timm opencv-python
+
+
+If you want to batch compress images using [Zstandard](https://github.com/facebook/zstd), use the package manager of your operating system to install it:
+
+    sudo apt-get install zstd    # for Linux
+    brew install zstd            # for macOS
+    choco install zstandard      # for Windows
+
 
 ## Usage
 
@@ -132,16 +128,15 @@ To use the plugin, start napari in the activated virtual environment with this t
 
     mamba run -n napari-tmidas napari
 
-You can find the installed plugin here:
-
-![image](https://github.com/user-attachments/assets/504db09a-d66e-49eb-90cd-3237024d9d7a)
-
+You can then find the installed plugin in the Plugins tab.
 
 ### Microscopy Image Conversion
 
 You can start this pipeline via `Plugins > T-MIDAS > Batch Microscopy Image Conversion`. Currently, this pipeline supports the conversion of `.nd2, .lif, .ndpi, .czi` and acquifer data. After scanning a folder of your choice for microscopy image data, select a file in the first column of the table and preview and export any image data it contains.
 
-![image](https://github.com/user-attachments/assets/e377ca71-2f30-447d-825e-d2feebf7061b)
+
+<img src="https://github.com/user-attachments/assets/e377ca71-2f30-447d-825e-d2feebf7061b" alt="Microscopy Image Conversion Widget" style="width:75%; height:auto;">
+
 
 ### Image Processing
 
@@ -149,7 +144,7 @@ You can start this pipeline via `Plugins > T-MIDAS > Batch Microscopy Image Conv
 
 ![image](https://github.com/user-attachments/assets/41ecb689-9abe-4371-83b5-9c5eb37069f9)
 
-2. As a result, a table appears with the found images.
+2. As a result, a table appears with the found images. You can click on them to inspect them in the viewer.
 
 ![image](https://github.com/user-attachments/assets/8360942a-be8f-49ec-bc25-385ee43bd601)
 
@@ -158,26 +153,28 @@ You can start this pipeline via `Plugins > T-MIDAS > Batch Microscopy Image Conv
 ![image](https://github.com/user-attachments/assets/05929660-6672-4f76-89da-4f17749ccfad)
 
 4. You can click on the images in the table to show them in the viewer. For example first click on one of the `Original Files`, and then the corresponding `Processed File` to see an overlay.
+   
+<img src="https://github.com/user-attachments/assets/cfe84828-c1cc-4196-9a53-5dfb82d5bfce" alt="Image Processing Widget" style="width:75%; height:auto;">
 
-![image](https://github.com/user-attachments/assets/cfe84828-c1cc-4196-9a53-5dfb82d5bfce)
 
 Note that whenever you click on an `Original File` or `Processed File` in the table, it will replace the one that is currently shown in the viewer. So naturally, you'd first select the original image, and then the processed image to correctly see the image pair that you want to inspect.
 
 ### Batch Label Inspection
 If you have already segmented a folder full of images and now you want to maybe inspect and edit each label image, you can use the `Plugins > T-MIDAS > Batch Label Inspection`, which automatically saves your changes to the existing label image once you click the `Save Changes and Continue` button (bottom right).
 
-![image](https://github.com/user-attachments/assets/0bf8c6ae-4212-449d-8183-e91b23ba740e)
+<img src="https://github.com/user-attachments/assets/0bf8c6ae-4212-449d-8183-e91b23ba740e" alt="Batch Label Inspection Widget" style="width:75%; height:auto;">
+
 
 ### Crop Anything
-This pipeline combines the Segment Anything Model (SAM) for automatic object detection with an interactive interface for selecting and cropping multiple objects from images. To launch the widget, open `Plugins > T-MIDAS > Batch Crop Anything`
+This pipeline combines the Segment Anything Model (SAM) for automatic object detection with an interactive interface for selecting and cropping multiple objects from images. To launch the widget, open `Plugins > T-MIDAS > Batch Crop Anything`. Click the image below to see a video demo.
+
+<img src="https://github.com/user-attachments/assets/6d72c2a2-1064-4a27-b398-a9b86fcbc443" alt="Crop Anything Widget" style="width:75%; height:auto;">
 
-![image](https://github.com/user-attachments/assets/6d72c2a2-1064-4a27-b398-a9b86fcbc443)
 
 ### ROI Colocalization
 This pipeline quantifies colocalization between labeled regions of interest (ROIs) across multiple image channels. It determines the extent of overlap between ROIs in a reference channel and those in one or two other channels. The output is a table of colocalization counts. Optionally, the size of reference channel ROIs, as well as the total or median size of colocalizing ROIs in the other channels, can be included. Colocalization is determined using Boolean masking. The number of colocalizing instances is determined by counting unique label IDs within the overlapping regions. Typically, the reference channel contains larger structures, while other channels contain smaller, potentially nested, structures. For example, the reference channel might contain cell bodies, with the second and third channels containing nuclei and sub-nuclear objects, respectively.
 
-![napari-tmidas_coloc_pipeline](https://github.com/user-attachments/assets/2f9022a0-7b88-4588-a448-250f07a634d7)
-
+<img src="https://github.com/user-attachments/assets/2f9022a0-7b88-4588-a448-250f07a634d7" alt="ROI Colocalization Widget" style="width:75%; height:auto;">
 
 ## Contributing
 

{napari_tmidas-0.1.8 → napari_tmidas-0.1.9}/README.md

@@ -6,34 +6,14 @@
 [![tests](https://github.com/macromeer/napari-tmidas/workflows/tests/badge.svg)](https://github.com/macromeer/napari-tmidas/actions)
 [![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-tmidas)](https://napari-hub.org/plugins/napari-tmidas)
 <!-- [![codecov](https://codecov.io/gh/macromeer/napari-tmidas/branch/main/graph/badge.svg)](https://codecov.io/gh/macromeer/napari-tmidas) -->
-The `napari-tmidas` plugin consists of a growing collection of pipelines for fast batch processing of microscopy images. This is a WIP and based on the CLI version of [T-MIDAS](https://github.com/MercaderLabAnatomy/T-MIDAS).
-
-## Feature Overview
-
-1. **Image Processing**
-   - Process image folders with: Gamma correction, Z-projection, channel splitting, Gaussian/median filters, thresholding (Otsu/manual), and label cleaning
-
-2. **Label Inspection**
-   - Review and edit label images with auto-save
-
-3. **Microscopy Image Conversion**
-   - Convert .nd2/.lif/.ndpi/.czi/acquifer → .tif/.zarr with metadata preservation
-
-4. **Crop Anything**
-   - Interactive ROI selection via click interface
-
-5. **ROI Colocalization**
-   - Count colocalized labels across multiple channels
-
-
-
-### Coming Soon
-New features arriving April 2025
+The `napari-tmidas` plugin consists of a growing collection of pipelines for fast batch processing of confocal and whole slide microscopy images of biological tissues. This is a WIP and based on the CLI version of [T-MIDAS](https://github.com/MercaderLabAnatomy/T-MIDAS).
 
+## Features
+Currently, napari-tmidas provides pipelines as widgets for batch image conversion / cropping / processing, ROI colocalization and label inspection (cf. [Usage](#usage) below).
 
 ## Installation
 
-First install Napari in a virtual environment:
+First, install Napari in a virtual environment:
 
     mamba create -y -n napari-tmidas -c conda-forge python=3.11 tqdm
     mamba activate napari-tmidas
@@ -43,19 +23,27 @@ Now you can install `napari-tmidas` via [pip]:
 
     pip install napari-tmidas
 
-To install the latest development version:
+It is recommended to install the latest development version:
 
     pip install git+https://github.com/macromeer/napari-tmidas.git
 
 ### Dependencies
-To use the Batch Microscopy Image Conversion pipeline, we need some libraries to read microscopy formats and to write ome-zarr:
 
-    pip install nd2 readlif tiffslide pylibCZIrw acquifer-napari ome-zarr napari-ome-zarr
+To use the Batch Microscopy Image Conversion pipeline, we need some libraries to read microscopy formats:
+
+    pip install nd2 readlif tiffslide pylibCZIrw acquifer-napari
 
 For the Batch Crop Anything pipeline, we need to install MobileSAM and its dependencies:
 
     pip install git+https://github.com/ChaoningZhang/MobileSAM.git
-    pip install torch torchvision timm opencv-python
+
+
+If you want to batch compress images using [Zstandard](https://github.com/facebook/zstd), use the package manager of your operating system to install it:
+
+    sudo apt-get install zstd    # for Linux
+    brew install zstd            # for macOS
+    choco install zstandard      # for Windows
+
 
 ## Usage
 
@@ -63,16 +51,15 @@ To use the plugin, start napari in the activated virtual environment with this t
 
     mamba run -n napari-tmidas napari
 
-You can find the installed plugin here:
-
-![image](https://github.com/user-attachments/assets/504db09a-d66e-49eb-90cd-3237024d9d7a)
-
+You can then find the installed plugin in the Plugins tab.
 
 ### Microscopy Image Conversion
 
 You can start this pipeline via `Plugins > T-MIDAS > Batch Microscopy Image Conversion`. Currently, this pipeline supports the conversion of `.nd2, .lif, .ndpi, .czi` and acquifer data. After scanning a folder of your choice for microscopy image data, select a file in the first column of the table and preview and export any image data it contains.
 
-![image](https://github.com/user-attachments/assets/e377ca71-2f30-447d-825e-d2feebf7061b)
+
+<img src="https://github.com/user-attachments/assets/e377ca71-2f30-447d-825e-d2feebf7061b" alt="Microscopy Image Conversion Widget" style="width:75%; height:auto;">
+
 
 ### Image Processing
 
@@ -80,7 +67,7 @@ You can start this pipeline via `Plugins > T-MIDAS > Batch Microscopy Image Conv
 
 ![image](https://github.com/user-attachments/assets/41ecb689-9abe-4371-83b5-9c5eb37069f9)
 
-2. As a result, a table appears with the found images.
+2. As a result, a table appears with the found images. You can click on them to inspect them in the viewer.
 
 ![image](https://github.com/user-attachments/assets/8360942a-be8f-49ec-bc25-385ee43bd601)
 
@@ -89,26 +76,28 @@ You can start this pipeline via `Plugins > T-MIDAS > Batch Microscopy Image Conv
 ![image](https://github.com/user-attachments/assets/05929660-6672-4f76-89da-4f17749ccfad)
 
 4. You can click on the images in the table to show them in the viewer. For example first click on one of the `Original Files`, and then the corresponding `Processed File` to see an overlay.
+   
+<img src="https://github.com/user-attachments/assets/cfe84828-c1cc-4196-9a53-5dfb82d5bfce" alt="Image Processing Widget" style="width:75%; height:auto;">
 
-![image](https://github.com/user-attachments/assets/cfe84828-c1cc-4196-9a53-5dfb82d5bfce)
 
 Note that whenever you click on an `Original File` or `Processed File` in the table, it will replace the one that is currently shown in the viewer. So naturally, you'd first select the original image, and then the processed image to correctly see the image pair that you want to inspect.
 
 ### Batch Label Inspection
 If you have already segmented a folder full of images and now you want to maybe inspect and edit each label image, you can use the `Plugins > T-MIDAS > Batch Label Inspection`, which automatically saves your changes to the existing label image once you click the `Save Changes and Continue` button (bottom right).
 
-![image](https://github.com/user-attachments/assets/0bf8c6ae-4212-449d-8183-e91b23ba740e)
+<img src="https://github.com/user-attachments/assets/0bf8c6ae-4212-449d-8183-e91b23ba740e" alt="Batch Label Inspection Widget" style="width:75%; height:auto;">
+
 
 ### Crop Anything
-This pipeline combines the Segment Anything Model (SAM) for automatic object detection with an interactive interface for selecting and cropping multiple objects from images. To launch the widget, open `Plugins > T-MIDAS > Batch Crop Anything`
+This pipeline combines the Segment Anything Model (SAM) for automatic object detection with an interactive interface for selecting and cropping multiple objects from images. To launch the widget, open `Plugins > T-MIDAS > Batch Crop Anything`. Click the image below to see a video demo.
+
+<img src="https://github.com/user-attachments/assets/6d72c2a2-1064-4a27-b398-a9b86fcbc443" alt="Crop Anything Widget" style="width:75%; height:auto;">
 
-![image](https://github.com/user-attachments/assets/6d72c2a2-1064-4a27-b398-a9b86fcbc443)
 
 ### ROI Colocalization
 This pipeline quantifies colocalization between labeled regions of interest (ROIs) across multiple image channels. It determines the extent of overlap between ROIs in a reference channel and those in one or two other channels. The output is a table of colocalization counts. Optionally, the size of reference channel ROIs, as well as the total or median size of colocalizing ROIs in the other channels, can be included. Colocalization is determined using Boolean masking. The number of colocalizing instances is determined by counting unique label IDs within the overlapping regions. Typically, the reference channel contains larger structures, while other channels contain smaller, potentially nested, structures. For example, the reference channel might contain cell bodies, with the second and third channels containing nuclei and sub-nuclear objects, respectively.
 
-![napari-tmidas_coloc_pipeline](https://github.com/user-attachments/assets/2f9022a0-7b88-4588-a448-250f07a634d7)
-
+<img src="https://github.com/user-attachments/assets/2f9022a0-7b88-4588-a448-250f07a634d7" alt="ROI Colocalization Widget" style="width:75%; height:auto;">
 
 ## Contributing
 

{napari_tmidas-0.1.8 → napari_tmidas-0.1.9}/pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "napari-tmidas"
 dynamic = ["version"]
-description = "Tissue Microscopy Image Data Analysis Suite"
+description = "A plugin for batch processing of confocal and whole-slide microscopy images of biological tissues"
 readme = "README.md"
 license = {file = "LICENSE"}
 authors = [
@@ -30,6 +30,14 @@ dependencies = [
     "qtpy",
     "scikit-image",
     "pyqt5",
+    "tqdm",
+    "scikit-image",
+    "ome-zarr",
+    "napari-ome-zarr",
+    "torch",
+    "torchvision",
+    "timm",
+    "opencv-python",
 ]
 
 [project.optional-dependencies]

{napari_tmidas-0.1.8 → napari_tmidas-0.1.9}/src/napari_tmidas/_crop_anything.py

@@ -29,6 +29,7 @@ from qtpy.QtWidgets import (
     QWidget,
 )
 from skimage.io import imread
+from skimage.transform import resize  # Added import for resize function
 from tifffile import imwrite
 
 
@@ -48,6 +49,7 @@ class BatchCropAnything:
         self.original_image = None
         self.segmentation_result = None
         self.current_image_for_segmentation = None
+        self.current_scale_factor = 1.0  # Added scale factor tracking
 
         # UI references
         self.image_layer = None
@@ -356,10 +358,41 @@ class BatchCropAnything:
             # Convert back to uint8
             image_gamma = (image_gamma * 255).astype(np.uint8)
 
+            # Check if the image is very large and needs downscaling
+            orig_shape = image_gamma.shape[:2]  # (height, width)
+
+            # Calculate image size in megapixels
+            image_mp = (orig_shape[0] * orig_shape[1]) / 1e6
+
+            # If image is larger than 2 megapixels, downscale it
+            max_mp = 2.0  # Maximum image size in megapixels
+            scale_factor = 1.0
+
+            if image_mp > max_mp:
+                scale_factor = np.sqrt(max_mp / image_mp)
+                new_height = int(orig_shape[0] * scale_factor)
+                new_width = int(orig_shape[1] * scale_factor)
+
+                self.viewer.status = f"Downscaling image from {orig_shape} to {(new_height, new_width)} for processing (scale: {scale_factor:.2f})"
+
+                # Resize the image for processing
+                image_gamma_resized = resize(
+                    image_gamma,
+                    (new_height, new_width),
+                    anti_aliasing=True,
+                    preserve_range=True,
+                ).astype(np.uint8)
+
+                # Store scale factor for later use
+                self.current_scale_factor = scale_factor
+            else:
+                image_gamma_resized = image_gamma
+                self.current_scale_factor = 1.0
+
             self.viewer.status = f"Generating segmentation with sensitivity {self.sensitivity} (gamma={gamma:.2f})..."
 
-            # Generate masks with gamma-corrected image
-            masks = self.mask_generator.generate(image_gamma)
+            # Generate masks with gamma-corrected and potentially resized image
+            masks = self.mask_generator.generate(image_gamma_resized)
             self.viewer.status = f"Generated {len(masks)} masks"
 
             if not masks:
@@ -390,9 +423,16 @@ class BatchCropAnything:
                 return
 
             # Process segmentation masks
-            self._process_segmentation_masks(
-                masks, self.current_image_for_segmentation.shape[:2]
-            )
+            # If image was downscaled, we need to ensure masks are upscaled correctly
+            if self.current_scale_factor < 1.0:
+                # Upscale the segmentation masks to match the original image dimensions
+                self._process_segmentation_masks_with_scaling(
+                    masks, self.current_image_for_segmentation.shape[:2]
+                )
+            else:
+                self._process_segmentation_masks(
+                    masks, self.current_image_for_segmentation.shape[:2]
+                )
 
             # Clear selected labels since segmentation has changed
             self.selected_labels = set()
@@ -475,6 +515,98 @@ class BatchCropAnything:
         # image_name = os.path.basename(self.images[self.current_index])
         self.viewer.status = f"Loaded image {self.current_index + 1}/{len(self.images)} - Found {len(masks)} segments"
 
+    # New method for handling scaled segmentation masks
+    def _process_segmentation_masks_with_scaling(self, masks, original_shape):
+        """Process segmentation masks with scaling to match the original image size."""
+        # Create label image from masks
+        # First determine the size of the mask predictions (which are at the downscaled resolution)
+        if not masks:
+            return
+
+        mask_shape = masks[0]["segmentation"].shape
+
+        # Create an empty label image at the downscaled resolution
+        downscaled_labels = np.zeros(mask_shape, dtype=np.uint32)
+        self.label_info = {}  # Reset label info
+
+        # Fill in the downscaled labels
+        for i, mask_data in enumerate(masks):
+            mask = mask_data["segmentation"]
+            label_id = i + 1  # Start label IDs from 1
+            downscaled_labels[mask] = label_id
+
+            # Store basic label info
+            area = np.sum(mask)
+            y_indices, x_indices = np.where(mask)
+            center_y = np.mean(y_indices) if len(y_indices) > 0 else 0
+            center_x = np.mean(x_indices) if len(x_indices) > 0 else 0
+
+            # Scale centers to original image coordinates
+            center_y_orig = center_y / self.current_scale_factor
+            center_x_orig = center_x / self.current_scale_factor
+
+            # Store label info at original scale
+            self.label_info[label_id] = {
+                "area": area
+                / (
+                    self.current_scale_factor**2
+                ),  # Approximate area in original scale
+                "center_y": center_y_orig,
+                "center_x": center_x_orig,
+                "score": mask_data.get("stability_score", 0),
+            }
+
+        # Upscale the labels to the original image size
+        upscaled_labels = resize(
+            downscaled_labels,
+            original_shape,
+            order=0,  # Nearest neighbor interpolation
+            preserve_range=True,
+            anti_aliasing=False,
+        ).astype(np.uint32)
+
+        # Sort labels by area (largest first)
+        self.label_info = dict(
+            sorted(
+                self.label_info.items(),
+                key=lambda item: item[1]["area"],
+                reverse=True,
+            )
+        )
+
+        # Save segmentation result
+        self.segmentation_result = upscaled_labels
+
+        # Remove existing label layer if exists
+        for layer in list(self.viewer.layers):
+            if isinstance(layer, Labels) and "Segmentation" in layer.name:
+                self.viewer.layers.remove(layer)
+
+        # Add label layer to viewer
+        self.label_layer = self.viewer.add_labels(
+            upscaled_labels,
+            name=f"Segmentation ({os.path.basename(self.images[self.current_index])})",
+            opacity=0.7,
+        )
+
+        # Make the label layer active by default
+        self.viewer.layers.selection.active = self.label_layer
+
+        # Disconnect existing callbacks if any
+        if (
+            hasattr(self, "label_layer")
+            and self.label_layer is not None
+            and hasattr(self.label_layer, "mouse_drag_callbacks")
+        ):
+            # Remove old callbacks
+            for callback in list(self.label_layer.mouse_drag_callbacks):
+                self.label_layer.mouse_drag_callbacks.remove(callback)
+
+        # Connect mouse click event to label selection
+        self.label_layer.mouse_drag_callbacks.append(self._on_label_clicked)
+
+        self.viewer.status = f"Loaded image {self.current_index + 1}/{len(self.images)} - Found {len(masks)} segments"
+
     # --------------------------------------------------
     # Label Selection and UI Elements
     # --------------------------------------------------

{napari_tmidas-0.1.8 → napari_tmidas-0.1.9}/src/napari_tmidas/_file_conversion.py

@@ -1105,19 +1105,21 @@ class ConversionWorker(QThread):
                 )
                 file_size_GB = estimated_size_bytes / (1024**3)
 
-                # If file is very large (>4GB), force zarr format regardless of setting
+                # Determine format
                 use_zarr = self.use_zarr
-                if file_size_GB > 4:
-                    use_zarr = True
-                    if not self.use_zarr:
-                        print(
-                            f"File size ({file_size_GB:.2f}GB) exceeds 4GB limit for TIF, automatically using ZARR format"
-                        )
-                        self.file_done.emit(
-                            filepath,
-                            True,
-                            f"File size ({file_size_GB:.2f}GB) exceeds 4GB, using ZARR format",
-                        )
+                # If file is very large (>4GB) and user didn't explicitly choose TIF,
+                # auto-switch to ZARR format
+                if file_size_GB > 4 and not self.use_zarr:
+                    # Recommend ZARR format but respect user's choice by still allowing TIF
+                    print(
+                        f"File size ({file_size_GB:.2f}GB) exceeds 4GB, ZARR format is recommended but using TIF with BigTIFF format"
+                    )
+                    self.file_done.emit(
+                        filepath,
+                        True,
+                        f"File size ({file_size_GB:.2f}GB) exceeds 4GB, using TIF with BigTIFF format",
+                    )
+
                 # Set up the output path
                 if use_zarr:
                     output_path = os.path.join(
@@ -1171,12 +1173,22 @@ class ConversionWorker(QThread):
     def _save_tif(
         self, image_data: np.ndarray, output_path: str, metadata: dict = None
     ):
-        """Enhanced TIF saving with proper dimension handling"""
+        """Enhanced TIF saving with proper dimension handling and BigTIFF support"""
         import tifffile
 
         print(f"Saving TIF file: {output_path}")
         print(f"Image data shape: {image_data.shape}")
 
+        # Check if this is a large file that needs BigTIFF
+        estimated_size_bytes = np.prod(image_data.shape) * image_data.itemsize
+        file_size_GB = estimated_size_bytes / (1024**3)
+        use_bigtiff = file_size_GB > 4
+
+        if use_bigtiff:
+            print(
+                f"File size ({file_size_GB:.2f}GB) exceeds 4GB, using BigTIFF format"
+            )
+
         if metadata:
             print(f"Metadata keys: {list(metadata.keys())}")
             if "axes" in metadata:
@@ -1198,7 +1210,12 @@ class ConversionWorker(QThread):
         # Basic save if no metadata
         if metadata is None:
             print("No metadata provided, using basic save")
-            tifffile.imwrite(output_path, image_data, compression="zstd")
+            tifffile.imwrite(
+                output_path,
+                image_data,
+                compression="zlib",
+                bigtiff=use_bigtiff,
+            )
             return
 
         # Get image dimensions and axis order
@@ -1261,7 +1278,10 @@ class ConversionWorker(QThread):
                     print(f"Error reordering dimensions: {e}")
                     # Fall back to simple save without reordering
                     tifffile.imwrite(
-                        output_path, image_data, compression="zstd"
+                        output_path,
+                        image_data,
+                        compression="zlib",
+                        bigtiff=use_bigtiff,
                     )
                     return
 
@@ -1287,7 +1307,8 @@ class ConversionWorker(QThread):
                     output_path,
                     image_data,
                     resolution=resolution,
-                    compression="zstd",
+                    compression="zlib",
+                    bigtiff=use_bigtiff,
                 )
             else:
                 # Hyperstack case
@@ -1306,14 +1327,15 @@ class ConversionWorker(QThread):
                     imagej=True,
                     resolution=resolution,
                     metadata=imagej_metadata,
-                    compression="zstd",
+                    compression="zlib",
+                    bigtiff=use_bigtiff,
                 )
 
             print(f"Successfully saved TIF file: {output_path}")
         except (ValueError, FileNotFoundError) as e:
             print(f"Error saving TIF file: {e}")
             # Try simple save as fallback
-            tifffile.imwrite(output_path, image_data)
+            tifffile.imwrite(output_path, image_data, bigtiff=use_bigtiff)
 
     def _save_zarr(
         self, image_data: np.ndarray, output_path: str, metadata: dict = None