update README.md to reflect new features, usage instructions, and supported formats

README.md

@@ -1,39 +1,96 @@
 # BioFormatsImageInfo
 
-Metadata extraction tool based on Bio-Formats
+[![Maven](https://img.shields.io/badge/Java-1.8+-blue.svg)](https://www.oracle.com/java/)
+[![Bio-Formats](https://img.shields.io/badge/Bio--Formats-8.3.0-green.svg)](https://www.openmicroscopy.org/bio-formats/)
 
-## make package
+BioFormatsImageInfo is a metadata extraction and thumbnail generation tool for biomedical images, based on the [Bio-Formats](https://www.openmicroscopy.org/bio-formats/) library. It supports over 150 image formats and can be used both as a command-line tool and as a Java library.
+
+## Features
+
+-   **Wide Format Support**: Leverages Bio-Formats' extensive format support
+-   **Metadata Extraction**: Outputs detailed image information in JSON format
+-   **Thumbnail Generation**: Creates high-quality thumbnail images
+-   **Command-Line Ready**: Suitable for batch processing and scripting
+-   **Library Integration**: Can be embedded into Java applications
+
+## Requirements
+
+-   Java 1.8 or higher
+-   Maven 3.0 or higher (for building)
+
+## Installation & Build
+
+Clone and build the project:
 
 ```shell
+git clone [repository-url]
+cd bioformats-imageinfo
 mvn package
 ```
 
-## run
+After the build completes, the following files will be generated:
+
+-   `target/dist/` - Executable distribution
+-   `target/bioformats-imageinfo-1.2.6.jar` - Standard JAR file
+-   `target/bioformats-imageinfo-1.2.6-jar-with-dependencies.jar` - Fat JAR with dependencies
+
+## Usage
+
+### Command Line Execution
+
+#### Using Executable Script (Recommended)
 
 ```shell
-./target/dist/bin/bioformats-imageinfo "[OPTION]" "[path to image file]"
+./target/dist/bin/bioformats-imageinfo [OPTION] [path to image file]
 ```
 
-### run by jar
+#### Running from JAR File
 
 ```shell
-java -jar ./target/dist/lib/bioformats-imageinfo-1.2.5.jar "[OPTION]" "[path to image file]"
+java -jar ./target/dist/lib/bioformats-imageinfo-1.2.6.jar [OPTION] [path to image file]
 ```
 
-### run by fat jar
+#### Running from Fat JAR
 
 ```shell
-java -jar ./target/bioformats-imageinfo-1.2.5-jar-with-dependencies.jar "[OPTION]" "[path to image file]"
+java -jar ./target/bioformats-imageinfo-1.2.6-jar-with-dependencies.jar [OPTION] [path to image file]
 ```
 
-### OPTION
+### Options
+
+| Option | Description                          |
+| ------ | ------------------------------------ |
+| `-M`   | Output metadata in JSON format       |
+| `-T`   | Generate and output thumbnail images |
+
+### Usage Examples
 
 ```shell
--M output metadata
--T output thumbnail
+# Extract metadata
+./target/dist/bin/bioformats-imageinfo -M sample.tif
+
+# Generate thumbnail
+./target/dist/bin/bioformats-imageinfo -T sample.tif
+
+# Output both metadata and thumbnail
+./target/dist/bin/bioformats-imageinfo -M -T sample.tif
 ```
 
-## library usage
+## Library Usage
+
+Example of using as a library in Java applications:
+
+### Adding Dependencies
+
+```xml
+<dependency>
+    <groupId>jp.riken.neurodata.tools.BioFormatsImageInfo</groupId>
+    <artifactId>bioformats-imageinfo</artifactId>
+    <version>1.2.6</version>
+</dependency>
+```
+
+### Sample Code
 
 ```java
 import java.util.LinkedHashMap;
@@ -42,16 +99,89 @@ import jp.riken.neurodata.tools.BioFormatsImageInfo;
 import jp.riken.neurodata.tools.BioFormatsImageException;
 import jp.riken.neurodata.tools.BioFormatsImageThumbnail;
 
-String path = "[path to image file]";
+// Path to image file
+String path = "path/to/your/image.tif";
 String format = "";
-Map<String, Object> metadata = new LinkedHashMap<String, Object>();
-Map<String, Object> thumbnail = new LinkedHashMap<String, Object>();
+Map<String, Object> metadata = new LinkedHashMap<>();
+Map<String, Object> thumbnail = new LinkedHashMap<>();
 
 try {
-  format = BioFormatsImageInfo.readMetadata(path, metadata);
-  BioFormatsImageThumbnail.readThumbnail(path, thumbnail);
+    // Read metadata
+    format = BioFormatsImageInfo.readMetadata(path, metadata);
+
+    // Generate thumbnail
+    BioFormatsImageThumbnail.readThumbnail(path, thumbnail);
+
+    // Use results
+    System.out.println("Image format: " + format);
+    System.out.println("Metadata: " + metadata);
+    System.out.println("Thumbnail info: " + thumbnail);
+
 } catch (BioFormatsImageException e) {
-  // error occurred
-  e.printStackTrace();
+    // Error handling
+    System.err.println("Error occurred while processing image: " + e.getMessage());
+    e.printStackTrace();
 }
 ```
+
+## Supported Image Formats
+
+As this tool uses the Bio-Formats library, it supports a wide variety of biomedical image formats including:
+
+-   **Microscopy Images**: LSM, CZI, ND2, OIB, OIF, LIF, etc.
+-   **Common Images**: TIFF, JPEG, PNG, BMP, etc.
+-   **Medical Images**: DICOM
+-   **Others**: Over 150 formats
+
+For detailed format support information, please refer to the [Bio-Formats official website](https://docs.openmicroscopy.org/bio-formats/latest/supported-formats.html).
+
+## Output Formats
+
+### Metadata Output
+
+-   Structured metadata in JSON format
+-   Image size, pixel information, acquisition conditions, etc.
+-   Detailed information for each series
+
+### Thumbnail Output
+
+-   Thumbnail images in JPEG format
+-   Base64 encoding support for embedding
+-   Adjustable quality (default: 85%)
+
+## License
+
+Please refer to the `LICENSE.txt` file for the license of this project.
+
+## Development & Contribution
+
+Developed by the Neuroinformatics Unit, RIKEN Center for Brain Science. Contributions are welcome via pull requests or issues on the repository.
+
+-   **Developer**: Neuroinformatics Unit, RIKEN Center for Brain Science
+-   **Project URL**: https://neurodata.riken.jp
+
+## Troubleshooting
+
+### Common Issues
+
+1. **Out of Memory Error**
+
+    ```shell
+    java -Xmx4g -jar bioformats-imageinfo-1.2.6-jar-with-dependencies.jar -M image.tif
+    ```
+
+2. **Processing Large Files**
+
+    - Disable Bio-Formats debug mode to improve processing speed
+    - Adjust JVM heap size as needed
+
+3. **Format Support**
+    - For unsupported formats, check the latest Bio-Formats version for support status
+
+### Log Output Configuration
+
+When detailed logs are needed:
+
+```shell
+java -Dloci.common.DebugTools.enableLogging=true -jar bioformats-imageinfo-1.2.6-jar-with-dependencies.jar -M image.tif
+```

pom.xml

@@ -5,17 +5,18 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>jp.riken.neurodata.tools.BioFormatsImageInfo</groupId>
   <artifactId>bioformats-imageinfo</artifactId>
-  <version>1.2.5</version>
+  <version>1.2.6</version>
 
   <name>bioformats-imageinfo</name>
   <url>https://neurodata.riken.jp</url>
 
   <properties>
-    <bio-formats.version>8.2.0</bio-formats.version>
+    <bio-formats.version>8.3.0</bio-formats.version>
     <bioformats-imageinfo.mainClass>jp.riken.neurodata.tools.BioFormatsImageInfo</bioformats-imageinfo.mainClass>
 
-    <maven.compiler.source>1.8</maven.compiler.source>
-    <maven.compiler.target>1.8</maven.compiler.target>
+    <java.version>1.8</java.version>
+    <maven.compiler.source>${java.version}</maven.compiler.source>
+    <maven.compiler.target>${java.version}</maven.compiler.target>
 
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
@@ -39,7 +40,7 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-enforcer-plugin</artifactId>
-        <version>3.5.0</version>
+        <version>3.6.2</version>
         <executions>
           <execution>
             <id>enforce-maven</id>
@@ -49,7 +50,7 @@
             <configuration>
               <rules>
                 <requireMavenVersion>
-                  <version>3.2.5</version>
+                  <version>3.6.3</version>
                 </requireMavenVersion>
               </rules>
             </configuration>
@@ -59,7 +60,7 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-dependency-plugin</artifactId>
-        <version>3.8.1</version>
+        <version>3.9.0</version>
         <executions>
           <execution>
             <id>copy-dependencies</id>
@@ -140,7 +141,7 @@
       <plugin>
         <groupId>org.owasp</groupId>
         <artifactId>dependency-check-maven</artifactId>
-        <version>12.1.3</version>
+        <version>12.1.8</version>
         <executions>
           <execution>
             <goals>
@@ -174,7 +175,8 @@
     </repository>
     <repository>
       <id>unidata.releases</id>
-      <url>https://artifacts.unidata.ucar.edu/content/repositories/unidata-releases</url>
+      <name>Unidata Releases</name>
+      <url>https://artifacts.unidata.ucar.edu/content/repositories/unidata-releases/</url>
     </repository>
   </repositories>