I got inspired by @guijacquemet.bsky.social's idea of making regular posts on #bioimageanalysis tools and tips under #BIATooloftheday. Will try to complement his suggestions with as little overlap as possible under #BIAToolTip with a focus on #Fiji and #ImageJ and friends.
In the hope it helps
In the hope it helps
November 16, 2024 at 2:33 PM
I got inspired by @guijacquemet.bsky.social's idea of making regular posts on #bioimageanalysis tools and tips under #BIATooloftheday. Will try to complement his suggestions with as little overlap as possible under #BIAToolTip with a focus on #Fiji and #ImageJ and friends.
In the hope it helps
In the hope it helps
In Fiji / ImageJ you can check it under Image › Color › Simulate Color Blindness or using the indicated button in the image below via the LUT channels tool from the #Biovoxxel Figure Tools which has much more to offer and I will feature this in the next #BIAToolTip post.
November 17, 2024 at 12:28 PM
In Fiji / ImageJ you can check it under Image › Color › Simulate Color Blindness or using the indicated button in the image below via the LUT channels tool from the #Biovoxxel Figure Tools which has much more to offer and I will feature this in the next #BIAToolTip post.
#BIAToolTip No.12
I wanted to highlight information regarding Western Blot analysis which is often performed in questionable ways. If you google for tutorials online many instructions you find are often quite (!) incorrect 🤯. Here some literature links and a suitable tool: GelAnalyzer
I wanted to highlight information regarding Western Blot analysis which is often performed in questionable ways. If you google for tutorials online many instructions you find are often quite (!) incorrect 🤯. Here some literature links and a suitable tool: GelAnalyzer
Western blot analysis information
Dear all, Since once in a while the topic semi-quantitative Western blot analysis pops up and many people in biological sciences who do Western blots or gels are into that, I wanted to share some inf...
forum.image.sc
November 27, 2024 at 4:00 PM
#BIAToolTip No.12
I wanted to highlight information regarding Western Blot analysis which is often performed in questionable ways. If you google for tutorials online many instructions you find are often quite (!) incorrect 🤯. Here some literature links and a suitable tool: GelAnalyzer
I wanted to highlight information regarding Western Blot analysis which is often performed in questionable ways. If you google for tutorials online many instructions you find are often quite (!) incorrect 🤯. Here some literature links and a suitable tool: GelAnalyzer
#BIAToolTip No.10 (SPECIAL)
NEW release of #biovoxxel Figure Tools v4.0.0.
Now, interactive merge images can be created as mentioned here: bsky.app/profile/biov...
All channel combinations can be checked in the resulting SVG files when opened in the browser.
NEW release of #biovoxxel Figure Tools v4.0.0.
Now, interactive merge images can be created as mentioned here: bsky.app/profile/biov...
All channel combinations can be checked in the resulting SVG files when opened in the browser.
November 25, 2024 at 2:10 PM
#BIAToolTip No.10 (SPECIAL)
NEW release of #biovoxxel Figure Tools v4.0.0.
Now, interactive merge images can be created as mentioned here: bsky.app/profile/biov...
All channel combinations can be checked in the resulting SVG files when opened in the browser.
NEW release of #biovoxxel Figure Tools v4.0.0.
Now, interactive merge images can be created as mentioned here: bsky.app/profile/biov...
All channel combinations can be checked in the resulting SVG files when opened in the browser.
Btw., no time for a #BIAToolTip today. So, I cheat,... the book will be my tip of the day (even though not read yet... no risk, no fun)
December 2, 2024 at 3:15 PM
Btw., no time for a #BIAToolTip today. So, I cheat,... the book will be my tip of the day (even though not read yet... no risk, no fun)
#BIAToolTip No.7
The Ridge Detection plugin from @thorstenwagner.bsky.social is really nice tool gem to automatically detect line-like structures in regular sized images in 2D/3D.
Even though, not actively maintained anymore, it runs stable and does what it should.
The Ridge Detection plugin from @thorstenwagner.bsky.social is really nice tool gem to automatically detect line-like structures in regular sized images in 2D/3D.
Even though, not actively maintained anymore, it runs stable and does what it should.
Ridge Detection
The ImageJ wiki is a community-edited knowledge base on topics relating to ImageJ, a public domain program for processing and analyzing scientific images, and its ecosystem of derivatives and variants...
imagej.net
November 21, 2024 at 7:18 AM
#BIAToolTip No.7
The Ridge Detection plugin from @thorstenwagner.bsky.social is really nice tool gem to automatically detect line-like structures in regular sized images in 2D/3D.
Even though, not actively maintained anymore, it runs stable and does what it should.
The Ridge Detection plugin from @thorstenwagner.bsky.social is really nice tool gem to automatically detect line-like structures in regular sized images in 2D/3D.
Even though, not actively maintained anymore, it runs stable and does what it should.
#BIAToolTip No.4
Object separation in 2D via the default watershed algorithm in IJ often suffers from over- or under-fragmentation.
The "Adjustable Watershed" from Michael Schmid is a nice and simple alternative to improve object separation after classical binarization.
imagej.net/plugins/adju...
Object separation in 2D via the default watershed algorithm in IJ often suffers from over- or under-fragmentation.
The "Adjustable Watershed" from Michael Schmid is a nice and simple alternative to improve object separation after classical binarization.
imagej.net/plugins/adju...
Adjustable Watershed
The ImageJ wiki is a community-edited knowledge base on topics relating to ImageJ, a public domain program for processing and analyzing scientific images, and its ecosystem of derivatives and variants...
imagej.net
November 19, 2024 at 7:41 AM
#BIAToolTip No.4
Object separation in 2D via the default watershed algorithm in IJ often suffers from over- or under-fragmentation.
The "Adjustable Watershed" from Michael Schmid is a nice and simple alternative to improve object separation after classical binarization.
imagej.net/plugins/adju...
Object separation in 2D via the default watershed algorithm in IJ often suffers from over- or under-fragmentation.
The "Adjustable Watershed" from Michael Schmid is a nice and simple alternative to improve object separation after classical binarization.
imagej.net/plugins/adju...
Here's a #BIAToolTip for the weekend! As Tuco says in the movie, there are two kinds of processing for image quantification in the world - there's processing for intensity measurement, and there's processing for segmentation.
Know which way you'll go before choosing filters!
#bioimageanalysis
Know which way you'll go before choosing filters!
#bioimageanalysis
December 7, 2024 at 4:17 PM
Here's a #BIAToolTip for the weekend! As Tuco says in the movie, there are two kinds of processing for image quantification in the world - there's processing for intensity measurement, and there's processing for segmentation.
Know which way you'll go before choosing filters!
#bioimageanalysis
Know which way you'll go before choosing filters!
#bioimageanalysis
#BIAToolTip No.9
Catching the ball from @guijacquemet.bsky.social and his NeuroCyto LUTs post. The LUT Channels Tool from the #biovoxxel Figure Tools can be equipped with any LUTs in the IJ lut folder or your favorite LUTs in a subfolder. Comes with all IJ channel functions and a color blind test.
Catching the ball from @guijacquemet.bsky.social and his NeuroCyto LUTs post. The LUT Channels Tool from the #biovoxxel Figure Tools can be equipped with any LUTs in the IJ lut folder or your favorite LUTs in a subfolder. Comes with all IJ channel functions and a color blind test.
November 25, 2024 at 1:42 PM
#BIAToolTip No.9
Catching the ball from @guijacquemet.bsky.social and his NeuroCyto LUTs post. The LUT Channels Tool from the #biovoxxel Figure Tools can be equipped with any LUTs in the IJ lut folder or your favorite LUTs in a subfolder. Comes with all IJ channel functions and a color blind test.
Catching the ball from @guijacquemet.bsky.social and his NeuroCyto LUTs post. The LUT Channels Tool from the #biovoxxel Figure Tools can be equipped with any LUTs in the IJ lut folder or your favorite LUTs in a subfolder. Comes with all IJ channel functions and a color blind test.
#BIAToolTip No.14
The Color Inspector 3D is a super useful tool to visualize color distribution in different color spaces for RGB images and can facilitate non-quantitative stain segmentation e.g. in IHC stainings. Available in #ImageJ and #Fiji
#bioimageanalysis
The Color Inspector 3D is a super useful tool to visualize color distribution in different color spaces for RGB images and can facilitate non-quantitative stain segmentation e.g. in IHC stainings. Available in #ImageJ and #Fiji
#bioimageanalysis
December 4, 2024 at 10:32 AM
#BIAToolTip No.14
The Color Inspector 3D is a super useful tool to visualize color distribution in different color spaces for RGB images and can facilitate non-quantitative stain segmentation e.g. in IHC stainings. Available in #ImageJ and #Fiji
#bioimageanalysis
The Color Inspector 3D is a super useful tool to visualize color distribution in different color spaces for RGB images and can facilitate non-quantitative stain segmentation e.g. in IHC stainings. Available in #ImageJ and #Fiji
#bioimageanalysis
#BIAToolTip No.3
In this thread I will introduce several of the #biovoxxel figure tools for Fiji that allow you to prepare images for scientific figures in line with GSP and preserving image quality as well as data integrity 100%
github.com/biovoxxel/Bi...
In this thread I will introduce several of the #biovoxxel figure tools for Fiji that allow you to prepare images for scientific figures in line with GSP and preserving image quality as well as data integrity 100%
github.com/biovoxxel/Bi...
GitHub - biovoxxel/BioVoxxel-Figure-Tools
Contribute to biovoxxel/BioVoxxel-Figure-Tools development by creating an account on GitHub.
github.com
November 18, 2024 at 7:25 AM
#BIAToolTip No.3
In this thread I will introduce several of the #biovoxxel figure tools for Fiji that allow you to prepare images for scientific figures in line with GSP and preserving image quality as well as data integrity 100%
github.com/biovoxxel/Bi...
In this thread I will introduce several of the #biovoxxel figure tools for Fiji that allow you to prepare images for scientific figures in line with GSP and preserving image quality as well as data integrity 100%
github.com/biovoxxel/Bi...
#BIAToolTip No.8
In addition to my last [#BIAToolTip No.8](bsky.app/profile/biov...) the Tubness Filter in ImageJ is an underestimated feature. It helps preprocessing line-like structures in 2D/3D for consecutive segmentation/tracing. It can also serve for object separation (coming up).
In addition to my last [#BIAToolTip No.8](bsky.app/profile/biov...) the Tubness Filter in ImageJ is an underestimated feature. It helps preprocessing line-like structures in 2D/3D for consecutive segmentation/tracing. It can also serve for object separation (coming up).
November 22, 2024 at 2:45 PM
#BIAToolTip No.8
In addition to my last [#BIAToolTip No.8](bsky.app/profile/biov...) the Tubness Filter in ImageJ is an underestimated feature. It helps preprocessing line-like structures in 2D/3D for consecutive segmentation/tracing. It can also serve for object separation (coming up).
In addition to my last [#BIAToolTip No.8](bsky.app/profile/biov...) the Tubness Filter in ImageJ is an underestimated feature. It helps preprocessing line-like structures in 2D/3D for consecutive segmentation/tracing. It can also serve for object separation (coming up).
#BIAToolTip No.5
3D Object segmentation mostly involves object separation.
Both works often better if you have isotropic voxels!
"Make 3D Image Isotropic" or "Make Voxel Isotropic" from the #biovoxxel 3D box does this straight forward.
forum.image.sc/t/imagej-nuc...
3D Object segmentation mostly involves object separation.
Both works often better if you have isotropic voxels!
"Make 3D Image Isotropic" or "Make Voxel Isotropic" from the #biovoxxel 3D box does this straight forward.
forum.image.sc/t/imagej-nuc...
November 20, 2024 at 8:28 AM
#BIAToolTip No.5
3D Object segmentation mostly involves object separation.
Both works often better if you have isotropic voxels!
"Make 3D Image Isotropic" or "Make Voxel Isotropic" from the #biovoxxel 3D box does this straight forward.
forum.image.sc/t/imagej-nuc...
3D Object segmentation mostly involves object separation.
Both works often better if you have isotropic voxels!
"Make 3D Image Isotropic" or "Make Voxel Isotropic" from the #biovoxxel 3D box does this straight forward.
forum.image.sc/t/imagej-nuc...
#BIAToolTip No.11 (actually more a processing tip)
A variance filter (or edge detection) can facilitate object segmentation in DIC or brightfield images. In the example below it even outperforms cellpose (even after various parameter tunings). Worth a test if custom model training is not feasible.
A variance filter (or edge detection) can facilitate object segmentation in DIC or brightfield images. In the example below it even outperforms cellpose (even after various parameter tunings). Worth a test if custom model training is not feasible.
November 26, 2024 at 1:44 PM
#BIAToolTip No.11 (actually more a processing tip)
A variance filter (or edge detection) can facilitate object segmentation in DIC or brightfield images. In the example below it even outperforms cellpose (even after various parameter tunings). Worth a test if custom model training is not feasible.
A variance filter (or edge detection) can facilitate object segmentation in DIC or brightfield images. In the example below it even outperforms cellpose (even after various parameter tunings). Worth a test if custom model training is not feasible.
#BIAToolTip No.2
Today, I would like to highlight the amazing IJ-wrapper 😎 for cellpose, omnipose and StarDist and more from
@romainguiet.bsky.social
and colleagues. It allows seamless integration of DL tools in a Fiji batch workflow including all imgae pre- and post-processing and analysis steps.
Today, I would like to highlight the amazing IJ-wrapper 😎 for cellpose, omnipose and StarDist and more from
@romainguiet.bsky.social
and colleagues. It allows seamless integration of DL tools in a Fiji batch workflow including all imgae pre- and post-processing and analysis steps.
November 17, 2024 at 8:05 AM
#BIAToolTip No.2
Today, I would like to highlight the amazing IJ-wrapper 😎 for cellpose, omnipose and StarDist and more from
@romainguiet.bsky.social
and colleagues. It allows seamless integration of DL tools in a Fiji batch workflow including all imgae pre- and post-processing and analysis steps.
Today, I would like to highlight the amazing IJ-wrapper 😎 for cellpose, omnipose and StarDist and more from
@romainguiet.bsky.social
and colleagues. It allows seamless integration of DL tools in a Fiji batch workflow including all imgae pre- and post-processing and analysis steps.
#BIAToolTip No.15
On Windows there is the ColourSimulator App which allows you to simulate on your screen with a slidable window to inspect design or images to check if those are inclusive for color deficient vision.
The #biovoxxel LUT Channels Tool provides a related functionality.
On Windows there is the ColourSimulator App which allows you to simulate on your screen with a slidable window to inspect design or images to check if those are inclusive for color deficient vision.
The #biovoxxel LUT Channels Tool provides a related functionality.
December 5, 2024 at 4:22 PM
#BIAToolTip No.15
On Windows there is the ColourSimulator App which allows you to simulate on your screen with a slidable window to inspect design or images to check if those are inclusive for color deficient vision.
The #biovoxxel LUT Channels Tool provides a related functionality.
On Windows there is the ColourSimulator App which allows you to simulate on your screen with a slidable window to inspect design or images to check if those are inclusive for color deficient vision.
The #biovoxxel LUT Channels Tool provides a related functionality.
#BIAToolTip No.6
Object or label separation, especially in 3D, are not trivial but the Label Splitter from the #biovoxxel 3D box if offering several algorithms that reduce bleed-over into neighboring objects.
Doc: biovoxxel.github.io/bv3dbox/#lab...
Video: youtu.be/H-NWVafWLfo?...
Object or label separation, especially in 3D, are not trivial but the Label Splitter from the #biovoxxel 3D box if offering several algorithms that reduce bleed-over into neighboring objects.
Doc: biovoxxel.github.io/bv3dbox/#lab...
Video: youtu.be/H-NWVafWLfo?...
BioVoxxel 3D Box - GPU-accellerated 2D and 3D Image Processing and Analysis
YouTube video by Jan Brocher
youtu.be
November 20, 2024 at 8:28 AM
#BIAToolTip No.6
Object or label separation, especially in 3D, are not trivial but the Label Splitter from the #biovoxxel 3D box if offering several algorithms that reduce bleed-over into neighboring objects.
Doc: biovoxxel.github.io/bv3dbox/#lab...
Video: youtu.be/H-NWVafWLfo?...
Object or label separation, especially in 3D, are not trivial but the Label Splitter from the #biovoxxel 3D box if offering several algorithms that reduce bleed-over into neighboring objects.
Doc: biovoxxel.github.io/bv3dbox/#lab...
Video: youtu.be/H-NWVafWLfo?...
#BIAToolTip No. 1
In Fiji/ImageJ the shortcut ([Ctrl] +) [Shift] + [U] brings up the normally hidden Plugins › Utilities › Control Panel (by Cezar Tigaret)
This gives quick access to the complete Fiji menu and specific panes you use often can be detached by simple dragging ⌨️
In Fiji/ImageJ the shortcut ([Ctrl] +) [Shift] + [U] brings up the normally hidden Plugins › Utilities › Control Panel (by Cezar Tigaret)
This gives quick access to the complete Fiji menu and specific panes you use often can be detached by simple dragging ⌨️
![In Fiji/ImageJ the shortcut ([Ctrl] +) [Shift] + [U] brings up the normally hidden Plugins › Utilities › Control Panel (by Cezar Tigaret)
This gives quick access to the complete Fiji menu and specific panes you use often can be detached by simple dragging](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:sna6oe62hwiq7bfzo5nugkvu/bafkreiarpsqxmypun65f4qyqumnjv3gmmqsrt6w76tyxp3ljtsthb25bqm@jpeg)
November 16, 2024 at 2:33 PM
#BIAToolTip No. 1
In Fiji/ImageJ the shortcut ([Ctrl] +) [Shift] + [U] brings up the normally hidden Plugins › Utilities › Control Panel (by Cezar Tigaret)
This gives quick access to the complete Fiji menu and specific panes you use often can be detached by simple dragging ⌨️
In Fiji/ImageJ the shortcut ([Ctrl] +) [Shift] + [U] brings up the normally hidden Plugins › Utilities › Control Panel (by Cezar Tigaret)
This gives quick access to the complete Fiji menu and specific panes you use often can be detached by simple dragging ⌨️
For today's #BIATooloftheday #BIAToolTip, a great way to dip your toe into powerful analysis tools. There are few things as zennish as watching a huge batch of open images disappear as a simple processing macro zips through the stack. I know batch mode goes faster but it's nice to watch. #Fiji
I got inspired by @guijacquemet.bsky.social's idea of making regular posts on #bioimageanalysis tools and tips under #BIATooloftheday. Will try to complement his suggestions with as little overlap as possible under #BIAToolTip with a focus on #Fiji and #ImageJ and friends.
In the hope it helps
In the hope it helps
November 20, 2024 at 11:30 PM
For today's #BIATooloftheday #BIAToolTip, a great way to dip your toe into powerful analysis tools. There are few things as zennish as watching a huge batch of open images disappear as a simple processing macro zips through the stack. I know batch mode goes faster but it's nice to watch. #Fiji
#BIAToolTip No.13
A Must-Know: the amazing CLIJ2 library from @haesleinhuepf.bsky.social and its IJ macro extensions make image processing and analyses of 2D/3D images on the GPU a breeze and super flexible. Huge function repository, a very neat clij2 assistant and super easy to macro record.
A Must-Know: the amazing CLIJ2 library from @haesleinhuepf.bsky.social and its IJ macro extensions make image processing and analyses of 2D/3D images on the GPU a breeze and super flexible. Huge function repository, a very neat clij2 assistant and super easy to macro record.
clij.github.io
GPU accelerated image processing for everyone
clij.github.io
November 28, 2024 at 2:43 PM
#BIAToolTip No.13
A Must-Know: the amazing CLIJ2 library from @haesleinhuepf.bsky.social and its IJ macro extensions make image processing and analyses of 2D/3D images on the GPU a breeze and super flexible. Huge function repository, a very neat clij2 assistant and super easy to macro record.
A Must-Know: the amazing CLIJ2 library from @haesleinhuepf.bsky.social and its IJ macro extensions make image processing and analyses of 2D/3D images on the GPU a breeze and super flexible. Huge function repository, a very neat clij2 assistant and super easy to macro record.