From 928d7133cd3878b1dd2aad869ffdd92df11bab56 Mon Sep 17 00:00:00 2001 From: cHaWaH Date: Mon, 5 Apr 2021 12:02:22 -0400 Subject: [PATCH 1/7] Update about.html Updated project description, citation, contact info --- templates/about.html | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/templates/about.html b/templates/about.html index eda92d5..bec9608 100644 --- a/templates/about.html +++ b/templates/about.html @@ -13,8 +13,13 @@

About

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Stomata Counter was born in the minds of Karl and Sven after a chance encounter at GSA 2016 in Denver, Colorado. Karl is an evolutionary biologist who studies plants at multiple time, geographic, and genomic scales. When he's not day dreaming about fossil plants, he spends most of his time studying the population genomics and evolutionary effects of hybridization in Poplars at the University of Vermont. Sven is a post-doc at Brown University and a whiz at the command line. Feel free to contact karl at kf [at] uvm.edu.

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Funding

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Stomata Counter started as a collaboration between the University of Vermont, Brown Univeristy, and the Smithsonian Institution. During Karl's dissertation, he was face with counting stomata from several thousand images and became determined not to do it manually. At GSA in 2016, Karl and Sven met and came up with a draft version of a CNN to estiamte counts of stomata. The extensive biological collections at the National Museum of Natural History and the United States Botanic garden were instrumental in extending the training data set to species outside if Populus.

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Feel free to contact Karl at karl.fetter [at] gmail.com with questions.

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How to Cite

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Please cite us if you use this tool for your research. +

Fetter, K.C., Eberhardt, S., Barclay, R.S., Wing, S. and Keller, S.R., 2019. StomataCounter: a neural network for automatic stomata identification and counting. New Phytologist, 223(3), pp.1671-1681. + +

Funding

Funding to create Stomata Counter was provided by an NSF grant to Dr. Stephen Keller (Award # 1461868) and a Smithsonian Institution Fellowship to Karl Fetter.

Source Code

The source code for StomataCounter is freely available on GitHub here. Setup requires a cuda8-capable GPU.

From 93ec93576573dbe9e51e8079f8786154ae4e5d85 Mon Sep 17 00:00:00 2001 From: cHaWaH Date: Fri, 9 Apr 2021 14:35:36 -0400 Subject: [PATCH 2/7] Updated manuscript url --- templates/index.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/templates/index.html b/templates/index.html index 82173d8..3c12e65 100644 --- a/templates/index.html +++ b/templates/index.html @@ -24,7 +24,7 @@

Stomata Counter

Welcome to StomataCounter!

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StomataCounter is a tool to work with plant epidermal micrographs to phenotype stomatal density. Supporting this method is a convolutional neural network trained about about 4,700 micrographs from 700 species of plants. You can read about how StomataCounter was developed and the tests we performed to validate StomataCounter's effectiveness in the preprint. We recommend you register an account with us so that you can return to your jobs after you leave the website.

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StomataCounter is a tool to work with plant epidermal micrographs to phenotype stomatal density. Supporting this method is a convolutional neural network trained about about 4,700 micrographs from 700 species of plants. You can read about how StomataCounter was developed and the tests we performed to validate StomataCounter's effectiveness in the New Phytologist manuscript. We recommend you register an account with us so that you can return to your jobs after you leave the website.

Instructions for using this site

The simplest way to use StomataCounter is to upload a jpeg using the upload button below, refresh your browser on the Dataset page after a few moments, then export the results using the Dataset operations pulldown menu.

Most users will have several hundred images to measure and uploading zip files of jpegs is more convencient. You can add more zipfiles or individual images to a dataset by navigating to that dataset's page and following the instructions to add more images. Once StomataCounter has finished detecting and counting stomata, you should view the results of all or a set of images to determine how well the method performed. Click on an image to view the result. You should annotate 50 or 100 images (or whatever number you're comfortable with) and view the correlation of human to automatic stomata counts. This is done by clicking on the Dataset operations drop down menu and selecting "Export correlation graph".

From a734e8ed14d47774cd5577369a5ab38412923bb6 Mon Sep 17 00:00:00 2001 From: cHaWaH Date: Thu, 29 Jul 2021 08:24:12 -0400 Subject: [PATCH 3/7] Updated caffemodel Update link to most recent caffemodel available. --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 5efa87a..455beb9 100644 --- a/README.md +++ b/README.md @@ -23,7 +23,7 @@ pyIMQ for image quality measures is also required and can be found here: https:/ If you prefer to not use the web service, a script can be used for batch processing locally. It can be used to input a set of images and output CSV file with stomata counts, and optionally create heatmaps of each processed image. -Download the pre-trained model weights from here [[Download]](https://drive.google.com/open?id=1StStt1aiN8q1rvSnSVY--87CQ8Z4Pf9b) and unzip the two files (sc_feb2019.caffemodel and sc_feb2019.prototxt). +Download the most current pre-trained model weights from here [[Download]](https://drive.google.com/file/d/18qirGnLD3oEpInyp1KAVf9ZsKf_MQkRb/view?usp=sharing) (alexnetftc_iter_5000_fcn.caffemodel and sc_feb2019.prototxt), or the published model weights here [[Download]](https://drive.google.com/open?id=1StStt1aiN8q1rvSnSVY--87CQ8Z4Pf9b) (sc_feb2019.caffemodel and sc_feb2019.prototxt) and unzip the two files. The processing command allows tweaking various settings such as the input scale and detection threshold. The interface is: From 7b3c2fdf3f383e5390cc1c3436ef582ace6edb63 Mon Sep 17 00:00:00 2001 From: cHaWaH Date: Thu, 29 Jul 2021 12:25:01 -0400 Subject: [PATCH 4/7] Update index.html Update users and give options --- templates/index.html | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/templates/index.html b/templates/index.html index 3c12e65..5c8ee5a 100644 --- a/templates/index.html +++ b/templates/index.html @@ -21,6 +21,21 @@

Stomata Counter

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+
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StomataCounter is experiencing an error

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Hi Users, as many of you have noticed, the image processor has not been working for some time. We apologize for the inconvenience and are working on a soltuion. Until the site is working, you have a few options. +

    +
  • Downlod and install the python pacakge from GitHub and work locally. Your output will be a csv of annotations and heatmaps and you won't have the ability to manually annotate images.
    • +
  • Use the python scripts that are installed on PlantIT. You still won't get the annotation UI, but you don't have to install anything.
    • +
  • If you want the annotation UI and don't care for the neural net annotations, use the hack users have discovered and upload images, then click on them to annotate. Your annotations will still be saved and you can export the results file nomally.
    • +
+ We are working to resolve the issues on the site and ask for your patience. Thanks for using the tool. +

+
+
+ {{ super() }} +

Welcome to StomataCounter!

From 7c0facaee8d0e1e4e3eed9a3d001cb97e60826a3 Mon Sep 17 00:00:00 2001 From: cHaWaH Date: Thu, 29 Jul 2021 14:12:01 -0400 Subject: [PATCH 5/7] Update index.html sp. --- templates/index.html | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/templates/index.html b/templates/index.html index 5c8ee5a..c6aba08 100644 --- a/templates/index.html +++ b/templates/index.html @@ -24,13 +24,13 @@

Stomata Counter

StomataCounter is experiencing an error

-

Hi Users, as many of you have noticed, the image processor has not been working for some time. We apologize for the inconvenience and are working on a soltuion. Until the site is working, you have a few options. +

Hi Users, as many of you have noticed, the image processor has not been working for some time. We apologize for the inconvenience and are working on a solution. Until the site is working, you have a few options.

    -
  • Downlod and install the python pacakge from GitHub and work locally. Your output will be a csv of annotations and heatmaps and you won't have the ability to manually annotate images.
    • +
  • Download and install the python package from GitHub and work locally. Your output will be a csv of annotations and heatmaps and you won't have the ability to manually annotate images.
  • Use the python scripts that are installed on PlantIT. You still won't get the annotation UI, but you don't have to install anything.
    • -
  • If you want the annotation UI and don't care for the neural net annotations, use the hack users have discovered and upload images, then click on them to annotate. Your annotations will still be saved and you can export the results file nomally.
    • +
  • If you want the annotation UI and don't care for the neural net annotations, use the hack users have discovered and upload images, then click on them to annotate. Your annotations will still be saved and you can export the results file normally.
- We are working to resolve the issues on the site and ask for your patience. Thanks for using the tool. + We are working to resolve the issues and ask for your patience.

From fa6805012bc69f9bf323627005b51d4ddeaa9763 Mon Sep 17 00:00:00 2001 From: Karl Date: Tue, 24 May 2022 17:34:24 -0400 Subject: [PATCH 6/7] Update index.html Removed error message --- templates/index.html | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/templates/index.html b/templates/index.html index c6aba08..5dc2297 100644 --- a/templates/index.html +++ b/templates/index.html @@ -21,18 +21,6 @@

Stomata Counter

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-
-

StomataCounter is experiencing an error

-

Hi Users, as many of you have noticed, the image processor has not been working for some time. We apologize for the inconvenience and are working on a solution. Until the site is working, you have a few options. -

    -
  • Download and install the python package from GitHub and work locally. Your output will be a csv of annotations and heatmaps and you won't have the ability to manually annotate images.
    • -
  • Use the python scripts that are installed on PlantIT. You still won't get the annotation UI, but you don't have to install anything.
    • -
  • If you want the annotation UI and don't care for the neural net annotations, use the hack users have discovered and upload images, then click on them to annotate. Your annotations will still be saved and you can export the results file normally.
    • -
- We are working to resolve the issues and ask for your patience. -

-
{{ super() }}
From 760b056bc563a6294a5e9f03ecacdb4a869618eb Mon Sep 17 00:00:00 2001 From: Karl Date: Tue, 7 Jun 2022 11:47:13 -0400 Subject: [PATCH 7/7] updated email --- templates/base.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/templates/base.html b/templates/base.html index a151b38..e971a2c 100644 --- a/templates/base.html +++ b/templates/base.html @@ -89,7 +89,7 @@

Maintenance on Sat 03/23/2019: We're running some maintenan {% block content %}
{% endblock %}