Release 3.6.1

Author: BiologyTools

BioLib.csproj

@@ -11,14 +11,14 @@
     <PackageIcon>banner.jpg</PackageIcon>
     <PackageReadmeFile>README.md</PackageReadmeFile>
     <RepositoryUrl>https://github.com/BiologyTools/BioLib</RepositoryUrl>
-    <AssemblyVersion>3.5.0</AssemblyVersion>
-    <FileVersion>3.5.0</FileVersion>
-    <PackageVersion>3.5.0</PackageVersion>
+    <AssemblyVersion>3.6.1</AssemblyVersion>
+    <FileVersion>3.6.1</FileVersion>
+    <PackageVersion>3.6.1</PackageVersion>
     <PackageLicenseExpression>GPL-3.0-only</PackageLicenseExpression>
     <PackageRequireLicenseAcceptance>True</PackageRequireLicenseAcceptance>
     <PackageProjectUrl>https://biologytools.github.io/</PackageProjectUrl>
     <PackageTags>Biology; ImageJ; Bio-Formats; OMERO; Image-Stacks; Microscopy; Whole-Slide-Image; QuPath; </PackageTags>
-    <PackageReleaseNotes>Added support for uploading images to OMERO.</PackageReleaseNotes>
+    <PackageReleaseNotes>Updated BioFormats.NET and other dependency updates also bug fixes.</PackageReleaseNotes>
     <Authors>Erik Repo</Authors>
     <Platforms>AnyCPU;x64</Platforms>
   </PropertyGroup>
@@ -36,16 +36,16 @@
   </ItemGroup>
 	<ItemGroup>
     <PackageReference Include="BitMiracle.LibTiff.NET" Version="2.4.660" />
-    <PackageReference Include="CS-Script" Version="4.8.21" />
+    <PackageReference Include="CS-Script" Version="4.9.7" />
     <PackageReference Include="ImageJ.NET" Version="154.0.0.2" />
     <PackageReference Include="Newtonsoft.Json" Version="13.0.3" />
-    <PackageReference Include="NuGet.Build.Tasks.Pack" Version="6.12.1">
+    <PackageReference Include="NuGet.Build.Tasks.Pack" Version="6.14.0">
       <PrivateAssets>all</PrivateAssets>
       <IncludeAssets>runtime; build; native; contentfiles; analyzers; buildtransitive</IncludeAssets>
     </PackageReference>
     <PackageReference Include="OMERO.NET" Version="1.0.5" />
-		<PackageReference Include="OpenSlideGTK" Version="2.1.1" />
-    <PackageReference Include="SixLabors.ImageSharp" Version="3.1.6" />
+    <PackageReference Include="OpenSlideGTK" Version="2.1.2" />
+    <PackageReference Include="SixLabors.ImageSharp" Version="3.1.10" />
   </ItemGroup>
   <ItemGroup>
     <None Update="banner.jpg">

Source/Bio.cs

@@ -3941,41 +3941,25 @@ public void To24Bit()
                 }
             }
             else
-            if (Buffers[0].PixelFormat == PixelFormat.Format16bppGrayScale || Buffers[0].PixelFormat == PixelFormat.Format8bppIndexed)
+            if (Buffers[0].PixelFormat == PixelFormat.Format16bppGrayScale)
             {
-                if (Buffers[0].PixelFormat == PixelFormat.Format16bppGrayScale)
+                //We run 8bit so we get 24 bit rgb.
+                for (int i = 0; i < Buffers.Count; i++)
                 {
-                    for (int i = 0; i < Buffers.Count; i++)
-                    {
-                        Buffers[i].Image = AForge.Imaging.Image.Convert16bppTo8bpp(Buffers[i]);
-                    }
-                    for (int c = 0; c < Channels.Count; c++)
-                    {
-                        for (int i = 0; i < Channels[c].range.Length; i++)
-                        {
-                            Channels[c].range[i].Min = (int)(((float)Channels[c].range[i].Min / (float)ushort.MaxValue) * byte.MaxValue);
-                            Channels[c].range[i].Max = (int)(((float)Channels[c].range[i].Max / (float)ushort.MaxValue) * byte.MaxValue);
-                        }
-                        Channels[c].BitsPerPixel = 8;
-                    }
+                    Buffers[i] = AForge.Imaging.Image.Convert16bppTo8bpp(Buffers[i]);
                 }
-                List<Bitmap> bfs = new List<Bitmap>();
-                if (Buffers.Count % 3 != 0)
-                    for (int i = 0; i < Buffers.Count; i++)
-                    {
-                        Bitmap bs = new Bitmap(ID, SizeX, SizeY, Buffers[i].PixelFormat, Buffers[i].Bytes, new ZCT(Buffers[i].Coordinate.Z, 0, Buffers[i].Coordinate.T), i, Buffers[i].Plane);
-                        Bitmap bbs = Bitmap.RGB8To24(bs);
-                        bs.Dispose();
-                        bs = null;
-                        bfs.Add(bbs);
-                    }
-                else
-                    for (int i = 0; i < Buffers.Count; i++)
-                    {
-                        Bitmap bs = Bitmap.GetBitmapRGB(Buffers[i].SizeX, Buffers[i].SizeY, PixelFormat.Format24bppRgb, Buffers[i].Bytes);
-                        bfs.Add(bs);
-                    }
-                Buffers = bfs;
+                To24Bit();
+            }
+            else if(Buffers[0].PixelFormat == PixelFormat.Format8bppIndexed)
+            {
+                List<Bitmap> bms = new List<Bitmap>();
+                //We run 8bit so we get 24 bit rgb.
+                for (int i = 0; i < Buffers.Count; i+=3)
+                {
+                    bms.Add(Bitmap.RGB8To24(new Bitmap[] { Buffers[i], Buffers[i+1], Buffers[i+2] }));
+                }
+                Buffers.Clear();
+                Buffers.AddRange(bms);
                 UpdateCoords(SizeZ, 1, SizeT);
             }
             foreach (var item in Buffers)
@@ -7529,7 +7513,7 @@ public static BioImage OpenOME(string file, int serie, bool tab, bool addToImage
                 b.bitsPerPixel = 16;
             b.series = serie;
             string order = reader.getDimensionOrder();
-            if (vips)
+            if (vips && tile)
                 OpenVips(b);
             //Lets get the channels and initialize them
             int i = 0;