Noah  Rowe

Noah Rowe

1594437240

SAEMI: Size Analysis of Electron Microscopy Images

This article is part 3 in my series detailing the use and development of SAEMI, a web application I created to perform high throughput quantitative analysis of electron microscopy images. You can check out the app here and its github here. Also, check out part 1 here (where I talk about the motivation behind creating this app) and part 2 here (where I give a walk-through of how to use the app). In this article, I will talk about how I trained a deep learning model to segment electron microscopy (EM) images for quantitative analysis of nanoparticles.

Choosing a Dataset

In order to train my model, I used a data-set taken from NFFA-EUROPE with over 20,000 Scanning Electron Microscopy (SEM) images taken from CNR-IOM in Trieste, Italy. This was one of the only large databases of EM images that I could actually access for free as you can imagine, most EM images are subject to strong copyright issues. The database consists of over 20,000 SEM images separated into 10 different categories (Biological, Fibres, Films_coated_Surface, MEMS_devices_and_electrodes, Nanowires, Particles, Patterned_surface, Porous_Sponge, Powder, Tips). For my training, however, I limited the training images to only be taken from the Particles category, which consisted of just under 4000 images.

One of the main reasons for this is because for almost all of the other categories, there wasn’t actually a way to obtain a useful size distribution from the image. For example, consider the EM image of fibres shown in Figure 1a. After segmenting the image, I could calculate the sizes of each fibre within the image, but you can also clearly see that the fibres extend out past the image. Therefore, the sizes I calculate are limited to what’s presented in the EM image and I can’t extract how long the fibres are from the image alone.

Image for post

Compare that to Figure 1b of the EM image of particles where the sizes shown in the image are clearly the size of the entire particle. Not only that, but images in this category tended to have the least degree of occlusion which made labeling and training much easier.

Within the Particles category, all the images were 768 pixels tall and 1024 pixels wide. Most of the particles were roughly circular in shape, with some images featuring hundreds of particles and other images featuring only one particle. The size of the particles in pixels were also quite varied due to differences in the magnification which ranged from 1 micron to 10 nanometers. An example of some of the particle images in the data-set is shown in Figure 2 below:

Image for post

Removing the Banners

To begin the training process, the raw images first had to be preprocessed. For the most part, this meant removing the banners that contained image metadata while retaining as much useful image data as possible. To accomplish this, I used a technique called “reflection padding”. Essentially, I replaced the banner region with its reflections along the top and bottom. An example of this is shown in Figure 3 with the reflections highlighted in red.

Image for post

Fig 3 Example of reflection padding. source: CNR-IOM (CC-BY)

In order to perform this transformation, however, I first had to detect the banner regions using OpenCV. To start, I took my image and created a binary mask of the image where all pixel values above 250 becomes 255 and all pixels below the threshold becomes 0. The code used to perform this is shown below along with the result in Figure 4.

import cv2

# convert image to grayscale
grayscale = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
# create binary mask based on threshold of 250
ret, binary = cv2.threshold(gray, 250, 255, cv2.THRESH_BINARY)

Image for post

While thresholding was already fairly effective in finding the banner region, I could still detect some elements of the image that weren’t part of the banner. To make sure only the banner region was detected and nothing else remained, I used erosion and dilation on the thresholded image to find where the vertical and horizontal lines are within the image. Erosion is an image processing technique where a kernel of a given size is scanned across an image. As the kernel travels along the image, the minimum pixel value is found and the pixel value at the center is replaced by that minimum. Dilation is a similar operation but the maximum pixel value is used instead.

The code to detect vertical and horizontal lines are shown below along with their results in Figure 5.

#machine-learning #data-science #data analysis

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SAEMI: Size Analysis of Electron Microscopy Images
Queenie  Davis

Queenie Davis

1653123600

EasyMDE: Simple, Beautiful and Embeddable JavaScript Markdown Editor

EasyMDE - Markdown Editor 

This repository is a fork of SimpleMDE, made by Sparksuite. Go to the dedicated section for more information.

A drop-in JavaScript text area replacement for writing beautiful and understandable Markdown. EasyMDE allows users who may be less experienced with Markdown to use familiar toolbar buttons and shortcuts.

In addition, the syntax is rendered while editing to clearly show the expected result. Headings are larger, emphasized words are italicized, links are underlined, etc.

EasyMDE also features both built-in auto saving and spell checking. The editor is entirely customizable, from theming to toolbar buttons and javascript hooks.

Try the demo

Preview

Quick access

Install EasyMDE

Via npm:

npm install easymde

Via the UNPKG CDN:

<link rel="stylesheet" href="https://unpkg.com/easymde/dist/easymde.min.css">
<script src="https://unpkg.com/easymde/dist/easymde.min.js"></script>

Or jsDelivr:

<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/easymde/dist/easymde.min.css">
<script src="https://cdn.jsdelivr.net/npm/easymde/dist/easymde.min.js"></script>

How to use

Loading the editor

After installing and/or importing the module, you can load EasyMDE onto the first textarea element on the web page:

<textarea></textarea>
<script>
const easyMDE = new EasyMDE();
</script>

Alternatively you can select a specific textarea, via JavaScript:

<textarea id="my-text-area"></textarea>
<script>
const easyMDE = new EasyMDE({element: document.getElementById('my-text-area')});
</script>

Editor functions

Use easyMDE.value() to get the content of the editor:

<script>
easyMDE.value();
</script>

Use easyMDE.value(val) to set the content of the editor:

<script>
easyMDE.value('New input for **EasyMDE**');
</script>

Configuration

Options list

  • autoDownloadFontAwesome: If set to true, force downloads Font Awesome (used for icons). If set to false, prevents downloading. Defaults to undefined, which will intelligently check whether Font Awesome has already been included, then download accordingly.
  • autofocus: If set to true, focuses the editor automatically. Defaults to false.
  • autosave: Saves the text that's being written and will load it back in the future. It will forget the text when the form it's contained in is submitted.
    • enabled: If set to true, saves the text automatically. Defaults to false.
    • delay: Delay between saves, in milliseconds. Defaults to 10000 (10 seconds).
    • submit_delay: Delay before assuming that submit of the form failed and saving the text, in milliseconds. Defaults to autosave.delay or 10000 (10 seconds).
    • uniqueId: You must set a unique string identifier so that EasyMDE can autosave. Something that separates this from other instances of EasyMDE elsewhere on your website.
    • timeFormat: Set DateTimeFormat. More information see DateTimeFormat instances. Default locale: en-US, format: hour:minute.
    • text: Set text for autosave.
  • autoRefresh: Useful, when initializing the editor in a hidden DOM node. If set to { delay: 300 }, it will check every 300 ms if the editor is visible and if positive, call CodeMirror's refresh().
  • blockStyles: Customize how certain buttons that style blocks of text behave.
    • bold: Can be set to ** or __. Defaults to **.
    • code: Can be set to ``` or ~~~. Defaults to ```.
    • italic: Can be set to * or _. Defaults to *.
  • unorderedListStyle: can be *, - or +. Defaults to *.
  • scrollbarStyle: Chooses a scrollbar implementation. The default is "native", showing native scrollbars. The core library also provides the "null" style, which completely hides the scrollbars. Addons can implement additional scrollbar models.
  • element: The DOM element for the textarea element to use. Defaults to the first textarea element on the page.
  • forceSync: If set to true, force text changes made in EasyMDE to be immediately stored in original text area. Defaults to false.
  • hideIcons: An array of icon names to hide. Can be used to hide specific icons shown by default without completely customizing the toolbar.
  • indentWithTabs: If set to false, indent using spaces instead of tabs. Defaults to true.
  • initialValue: If set, will customize the initial value of the editor.
  • previewImagesInEditor: - EasyMDE will show preview of images, false by default, preview for images will appear only for images on separate lines.
  • imagesPreviewHandler: - A custom function for handling the preview of images. Takes the parsed string between the parantheses of the image markdown ![]( ) as argument and returns a string that serves as the src attribute of the <img> tag in the preview. Enables dynamic previewing of images in the frontend without having to upload them to a server, allows copy-pasting of images to the editor with preview.
  • insertTexts: Customize how certain buttons that insert text behave. Takes an array with two elements. The first element will be the text inserted before the cursor or highlight, and the second element will be inserted after. For example, this is the default link value: ["[", "](http://)"].
    • horizontalRule
    • image
    • link
    • table
  • lineNumbers: If set to true, enables line numbers in the editor.
  • lineWrapping: If set to false, disable line wrapping. Defaults to true.
  • minHeight: Sets the minimum height for the composition area, before it starts auto-growing. Should be a string containing a valid CSS value like "500px". Defaults to "300px".
  • maxHeight: Sets fixed height for the composition area. minHeight option will be ignored. Should be a string containing a valid CSS value like "500px". Defaults to undefined.
  • onToggleFullScreen: A function that gets called when the editor's full screen mode is toggled. The function will be passed a boolean as parameter, true when the editor is currently going into full screen mode, or false.
  • parsingConfig: Adjust settings for parsing the Markdown during editing (not previewing).
    • allowAtxHeaderWithoutSpace: If set to true, will render headers without a space after the #. Defaults to false.
    • strikethrough: If set to false, will not process GFM strikethrough syntax. Defaults to true.
    • underscoresBreakWords: If set to true, let underscores be a delimiter for separating words. Defaults to false.
  • overlayMode: Pass a custom codemirror overlay mode to parse and style the Markdown during editing.
    • mode: A codemirror mode object.
    • combine: If set to false, will replace CSS classes returned by the default Markdown mode. Otherwise the classes returned by the custom mode will be combined with the classes returned by the default mode. Defaults to true.
  • placeholder: If set, displays a custom placeholder message.
  • previewClass: A string or array of strings that will be applied to the preview screen when activated. Defaults to "editor-preview".
  • previewRender: Custom function for parsing the plaintext Markdown and returning HTML. Used when user previews.
  • promptURLs: If set to true, a JS alert window appears asking for the link or image URL. Defaults to false.
  • promptTexts: Customize the text used to prompt for URLs.
    • image: The text to use when prompting for an image's URL. Defaults to URL of the image:.
    • link: The text to use when prompting for a link's URL. Defaults to URL for the link:.
  • uploadImage: If set to true, enables the image upload functionality, which can be triggered by drag and drop, copy-paste and through the browse-file window (opened when the user click on the upload-image icon). Defaults to false.
  • imageMaxSize: Maximum image size in bytes, checked before upload (note: never trust client, always check the image size at server-side). Defaults to 1024 * 1024 * 2 (2 MB).
  • imageAccept: A comma-separated list of mime-types used to check image type before upload (note: never trust client, always check file types at server-side). Defaults to image/png, image/jpeg.
  • imageUploadFunction: A custom function for handling the image upload. Using this function will render the options imageMaxSize, imageAccept, imageUploadEndpoint and imageCSRFToken ineffective.
    • The function gets a file and onSuccess and onError callback functions as parameters. onSuccess(imageUrl: string) and onError(errorMessage: string)
  • imageUploadEndpoint: The endpoint where the images data will be sent, via an asynchronous POST request. The server is supposed to save this image, and return a JSON response.
    • if the request was successfully processed (HTTP 200 OK): {"data": {"filePath": "<filePath>"}} where filePath is the path of the image (absolute if imagePathAbsolute is set to true, relative if otherwise);
    • otherwise: {"error": "<errorCode>"}, where errorCode can be noFileGiven (HTTP 400 Bad Request), typeNotAllowed (HTTP 415 Unsupported Media Type), fileTooLarge (HTTP 413 Payload Too Large) or importError (see errorMessages below). If errorCode is not one of the errorMessages, it is alerted unchanged to the user. This allows for server-side error messages. No default value.
  • imagePathAbsolute: If set to true, will treat imageUrl from imageUploadFunction and filePath returned from imageUploadEndpoint as an absolute rather than relative path, i.e. not prepend window.location.origin to it.
  • imageCSRFToken: CSRF token to include with AJAX call to upload image. For various instances like Django, Spring and Laravel.
  • imageCSRFName: CSRF token filed name to include with AJAX call to upload image, applied when imageCSRFToken has value, defaults to csrfmiddlewaretoken.
  • imageCSRFHeader: If set to true, passing CSRF token via header. Defaults to false, which pass CSRF through request body.
  • imageTexts: Texts displayed to the user (mainly on the status bar) for the import image feature, where #image_name#, #image_size# and #image_max_size# will replaced by their respective values, that can be used for customization or internationalization:
    • sbInit: Status message displayed initially if uploadImage is set to true. Defaults to Attach files by drag and dropping or pasting from clipboard..
    • sbOnDragEnter: Status message displayed when the user drags a file to the text area. Defaults to Drop image to upload it..
    • sbOnDrop: Status message displayed when the user drops a file in the text area. Defaults to Uploading images #images_names#.
    • sbProgress: Status message displayed to show uploading progress. Defaults to Uploading #file_name#: #progress#%.
    • sbOnUploaded: Status message displayed when the image has been uploaded. Defaults to Uploaded #image_name#.
    • sizeUnits: A comma-separated list of units used to display messages with human-readable file sizes. Defaults to B, KB, MB (example: 218 KB). You can use B,KB,MB instead if you prefer without whitespaces (218KB).
  • errorMessages: Errors displayed to the user, using the errorCallback option, where #image_name#, #image_size# and #image_max_size# will replaced by their respective values, that can be used for customization or internationalization:
    • noFileGiven: The server did not receive any file from the user. Defaults to You must select a file..
    • typeNotAllowed: The user send a file type which doesn't match the imageAccept list, or the server returned this error code. Defaults to This image type is not allowed..
    • fileTooLarge: The size of the image being imported is bigger than the imageMaxSize, or if the server returned this error code. Defaults to Image #image_name# is too big (#image_size#).\nMaximum file size is #image_max_size#..
    • importError: An unexpected error occurred when uploading the image. Defaults to Something went wrong when uploading the image #image_name#..
  • errorCallback: A callback function used to define how to display an error message. Defaults to (errorMessage) => alert(errorMessage).
  • renderingConfig: Adjust settings for parsing the Markdown during previewing (not editing).
    • codeSyntaxHighlighting: If set to true, will highlight using highlight.js. Defaults to false. To use this feature you must include highlight.js on your page or pass in using the hljs option. For example, include the script and the CSS files like:
      <script src="https://cdn.jsdelivr.net/highlight.js/latest/highlight.min.js"></script>
      <link rel="stylesheet" href="https://cdn.jsdelivr.net/highlight.js/latest/styles/github.min.css">
    • hljs: An injectible instance of highlight.js. If you don't want to rely on the global namespace (window.hljs), you can provide an instance here. Defaults to undefined.
    • markedOptions: Set the internal Markdown renderer's options. Other renderingConfig options will take precedence.
    • singleLineBreaks: If set to false, disable parsing GitHub Flavored Markdown (GFM) single line breaks. Defaults to true.
    • sanitizerFunction: Custom function for sanitizing the HTML output of Markdown renderer.
  • shortcuts: Keyboard shortcuts associated with this instance. Defaults to the array of shortcuts.
  • showIcons: An array of icon names to show. Can be used to show specific icons hidden by default without completely customizing the toolbar.
  • spellChecker: If set to false, disable the spell checker. Defaults to true. Optionally pass a CodeMirrorSpellChecker-compliant function.
  • inputStyle: textarea or contenteditable. Defaults to textarea for desktop and contenteditable for mobile. contenteditable option is necessary to enable nativeSpellcheck.
  • nativeSpellcheck: If set to false, disable native spell checker. Defaults to true.
  • sideBySideFullscreen: If set to false, allows side-by-side editing without going into fullscreen. Defaults to true.
  • status: If set to false, hide the status bar. Defaults to the array of built-in status bar items.
    • Optionally, you can set an array of status bar items to include, and in what order. You can even define your own custom status bar items.
  • styleSelectedText: If set to false, remove the CodeMirror-selectedtext class from selected lines. Defaults to true.
  • syncSideBySidePreviewScroll: If set to false, disable syncing scroll in side by side mode. Defaults to true.
  • tabSize: If set, customize the tab size. Defaults to 2.
  • theme: Override the theme. Defaults to easymde.
  • toolbar: If set to false, hide the toolbar. Defaults to the array of icons.
  • toolbarTips: If set to false, disable toolbar button tips. Defaults to true.
  • direction: rtl or ltr. Changes text direction to support right-to-left languages. Defaults to ltr.

Options example

Most options demonstrate the non-default behavior:

const editor = new EasyMDE({
    autofocus: true,
    autosave: {
        enabled: true,
        uniqueId: "MyUniqueID",
        delay: 1000,
        submit_delay: 5000,
        timeFormat: {
            locale: 'en-US',
            format: {
                year: 'numeric',
                month: 'long',
                day: '2-digit',
                hour: '2-digit',
                minute: '2-digit',
            },
        },
        text: "Autosaved: "
    },
    blockStyles: {
        bold: "__",
        italic: "_",
    },
    unorderedListStyle: "-",
    element: document.getElementById("MyID"),
    forceSync: true,
    hideIcons: ["guide", "heading"],
    indentWithTabs: false,
    initialValue: "Hello world!",
    insertTexts: {
        horizontalRule: ["", "\n\n-----\n\n"],
        image: ["![](http://", ")"],
        link: ["[", "](https://)"],
        table: ["", "\n\n| Column 1 | Column 2 | Column 3 |\n| -------- | -------- | -------- |\n| Text     | Text      | Text     |\n\n"],
    },
    lineWrapping: false,
    minHeight: "500px",
    parsingConfig: {
        allowAtxHeaderWithoutSpace: true,
        strikethrough: false,
        underscoresBreakWords: true,
    },
    placeholder: "Type here...",

    previewClass: "my-custom-styling",
    previewClass: ["my-custom-styling", "more-custom-styling"],

    previewRender: (plainText) => customMarkdownParser(plainText), // Returns HTML from a custom parser
    previewRender: (plainText, preview) => { // Async method
        setTimeout(() => {
            preview.innerHTML = customMarkdownParser(plainText);
        }, 250);

        return "Loading...";
    },
    promptURLs: true,
    promptTexts: {
        image: "Custom prompt for URL:",
        link: "Custom prompt for URL:",
    },
    renderingConfig: {
        singleLineBreaks: false,
        codeSyntaxHighlighting: true,
        sanitizerFunction: (renderedHTML) => {
            // Using DOMPurify and only allowing <b> tags
            return DOMPurify.sanitize(renderedHTML, {ALLOWED_TAGS: ['b']})
        },
    },
    shortcuts: {
        drawTable: "Cmd-Alt-T"
    },
    showIcons: ["code", "table"],
    spellChecker: false,
    status: false,
    status: ["autosave", "lines", "words", "cursor"], // Optional usage
    status: ["autosave", "lines", "words", "cursor", {
        className: "keystrokes",
        defaultValue: (el) => {
            el.setAttribute('data-keystrokes', 0);
        },
        onUpdate: (el) => {
            const keystrokes = Number(el.getAttribute('data-keystrokes')) + 1;
            el.innerHTML = `${keystrokes} Keystrokes`;
            el.setAttribute('data-keystrokes', keystrokes);
        },
    }], // Another optional usage, with a custom status bar item that counts keystrokes
    styleSelectedText: false,
    sideBySideFullscreen: false,
    syncSideBySidePreviewScroll: false,
    tabSize: 4,
    toolbar: false,
    toolbarTips: false,
});

Toolbar icons

Below are the built-in toolbar icons (only some of which are enabled by default), which can be reorganized however you like. "Name" is the name of the icon, referenced in the JavaScript. "Action" is either a function or a URL to open. "Class" is the class given to the icon. "Tooltip" is the small tooltip that appears via the title="" attribute. Note that shortcut hints are added automatically and reflect the specified action if it has a key bind assigned to it (i.e. with the value of action set to bold and that of tooltip set to Bold, the final text the user will see would be "Bold (Ctrl-B)").

Additionally, you can add a separator between any icons by adding "|" to the toolbar array.

NameActionTooltip
Class
boldtoggleBoldBold
fa fa-bold
italictoggleItalicItalic
fa fa-italic
strikethroughtoggleStrikethroughStrikethrough
fa fa-strikethrough
headingtoggleHeadingSmallerHeading
fa fa-header
heading-smallertoggleHeadingSmallerSmaller Heading
fa fa-header
heading-biggertoggleHeadingBiggerBigger Heading
fa fa-lg fa-header
heading-1toggleHeading1Big Heading
fa fa-header header-1
heading-2toggleHeading2Medium Heading
fa fa-header header-2
heading-3toggleHeading3Small Heading
fa fa-header header-3
codetoggleCodeBlockCode
fa fa-code
quotetoggleBlockquoteQuote
fa fa-quote-left
unordered-listtoggleUnorderedListGeneric List
fa fa-list-ul
ordered-listtoggleOrderedListNumbered List
fa fa-list-ol
clean-blockcleanBlockClean block
fa fa-eraser
linkdrawLinkCreate Link
fa fa-link
imagedrawImageInsert Image
fa fa-picture-o
tabledrawTableInsert Table
fa fa-table
horizontal-ruledrawHorizontalRuleInsert Horizontal Line
fa fa-minus
previewtogglePreviewToggle Preview
fa fa-eye no-disable
side-by-sidetoggleSideBySideToggle Side by Side
fa fa-columns no-disable no-mobile
fullscreentoggleFullScreenToggle Fullscreen
fa fa-arrows-alt no-disable no-mobile
guideThis linkMarkdown Guide
fa fa-question-circle
undoundoUndo
fa fa-undo
redoredoRedo
fa fa-redo

Toolbar customization

Customize the toolbar using the toolbar option.

Only the order of existing buttons:

const easyMDE = new EasyMDE({
    toolbar: ["bold", "italic", "heading", "|", "quote"]
});

All information and/or add your own icons

const easyMDE = new EasyMDE({
    toolbar: [
        {
            name: "bold",
            action: EasyMDE.toggleBold,
            className: "fa fa-bold",
            title: "Bold",
        },
        "italics", // shortcut to pre-made button
        {
            name: "custom",
            action: (editor) => {
                // Add your own code
            },
            className: "fa fa-star",
            title: "Custom Button",
            attributes: { // for custom attributes
                id: "custom-id",
                "data-value": "custom value" // HTML5 data-* attributes need to be enclosed in quotation marks ("") because of the dash (-) in its name.
            }
        },
        "|" // Separator
        // [, ...]
    ]
});

Put some buttons on dropdown menu

const easyMDE = new EasyMDE({
    toolbar: [{
                name: "heading",
                action: EasyMDE.toggleHeadingSmaller,
                className: "fa fa-header",
                title: "Headers",
            },
            "|",
            {
                name: "others",
                className: "fa fa-blind",
                title: "others buttons",
                children: [
                    {
                        name: "image",
                        action: EasyMDE.drawImage,
                        className: "fa fa-picture-o",
                        title: "Image",
                    },
                    {
                        name: "quote",
                        action: EasyMDE.toggleBlockquote,
                        className: "fa fa-percent",
                        title: "Quote",
                    },
                    {
                        name: "link",
                        action: EasyMDE.drawLink,
                        className: "fa fa-link",
                        title: "Link",
                    }
                ]
            },
        // [, ...]
    ]
});

Keyboard shortcuts

EasyMDE comes with an array of predefined keyboard shortcuts, but they can be altered with a configuration option. The list of default ones is as follows:

Shortcut (Windows / Linux)Shortcut (macOS)Action
Ctrl-'Cmd-'"toggleBlockquote"
Ctrl-BCmd-B"toggleBold"
Ctrl-ECmd-E"cleanBlock"
Ctrl-HCmd-H"toggleHeadingSmaller"
Ctrl-ICmd-I"toggleItalic"
Ctrl-KCmd-K"drawLink"
Ctrl-LCmd-L"toggleUnorderedList"
Ctrl-PCmd-P"togglePreview"
Ctrl-Alt-CCmd-Alt-C"toggleCodeBlock"
Ctrl-Alt-ICmd-Alt-I"drawImage"
Ctrl-Alt-LCmd-Alt-L"toggleOrderedList"
Shift-Ctrl-HShift-Cmd-H"toggleHeadingBigger"
F9F9"toggleSideBySide"
F11F11"toggleFullScreen"

Here is how you can change a few, while leaving others untouched:

const editor = new EasyMDE({
    shortcuts: {
        "toggleOrderedList": "Ctrl-Alt-K", // alter the shortcut for toggleOrderedList
        "toggleCodeBlock": null, // unbind Ctrl-Alt-C
        "drawTable": "Cmd-Alt-T", // bind Cmd-Alt-T to drawTable action, which doesn't come with a default shortcut
    }
});

Shortcuts are automatically converted between platforms. If you define a shortcut as "Cmd-B", on PC that shortcut will be changed to "Ctrl-B". Conversely, a shortcut defined as "Ctrl-B" will become "Cmd-B" for Mac users.

The list of actions that can be bound is the same as the list of built-in actions available for toolbar buttons.

Advanced use

Event handling

You can catch the following list of events: https://codemirror.net/doc/manual.html#events

const easyMDE = new EasyMDE();
easyMDE.codemirror.on("change", () => {
    console.log(easyMDE.value());
});

Removing EasyMDE from text area

You can revert to the initial text area by calling the toTextArea method. Note that this clears up the autosave (if enabled) associated with it. The text area will retain any text from the destroyed EasyMDE instance.

const easyMDE = new EasyMDE();
// ...
easyMDE.toTextArea();
easyMDE = null;

If you need to remove registered event listeners (when the editor is not needed anymore), call easyMDE.cleanup().

Useful methods

The following self-explanatory methods may be of use while developing with EasyMDE.

const easyMDE = new EasyMDE();
easyMDE.isPreviewActive(); // returns boolean
easyMDE.isSideBySideActive(); // returns boolean
easyMDE.isFullscreenActive(); // returns boolean
easyMDE.clearAutosavedValue(); // no returned value

How it works

EasyMDE is a continuation of SimpleMDE.

SimpleMDE began as an improvement of lepture's Editor project, but has now taken on an identity of its own. It is bundled with CodeMirror and depends on Font Awesome.

CodeMirror is the backbone of the project and parses much of the Markdown syntax as it's being written. This allows us to add styles to the Markdown that's being written. Additionally, a toolbar and status bar have been added to the top and bottom, respectively. Previews are rendered by Marked using GitHub Flavored Markdown (GFM).

SimpleMDE fork

I originally made this fork to implement FontAwesome 5 compatibility into SimpleMDE. When that was done I submitted a pull request, which has not been accepted yet. This, and the project being inactive since May 2017, triggered me to make more changes and try to put new life into the project.

Changes include:

  • FontAwesome 5 compatibility
  • Guide button works when editor is in preview mode
  • Links are now https:// by default
  • Small styling changes
  • Support for Node 8 and beyond
  • Lots of refactored code
  • Links in preview will open in a new tab by default
  • TypeScript support

My intention is to continue development on this project, improving it and keeping it alive.

Hacking EasyMDE

You may want to edit this library to adapt its behavior to your needs. This can be done in some quick steps:

  1. Follow the prerequisites and installation instructions in the contribution guide;
  2. Do your changes;
  3. Run gulp command, which will generate files: dist/easymde.min.css and dist/easymde.min.js;
  4. Copy-paste those files to your code base, and you are done.

Contributing

Want to contribute to EasyMDE? Thank you! We have a contribution guide just for you!


Author: Ionaru
Source Code: https://github.com/Ionaru/easy-markdown-editor
License: MIT license

#react-native #react 

Vern  Greenholt

Vern Greenholt

1594425900

SAEMI: Size Analysis of Electron Microscopy Images,

This article is part 2 in my series detailing the use and development of SAEMI, a web application I created to perform high throughput quantitative analysis of electron microscopy images. Check out part 1 here (where I go over the motivation behind the app) and part 3 here (where I go over how I trained my image segmentation model). You can also check out the app here and its Github here. In this article, I give a walk-through of how to use the app and obtain the best results.


So You Have an Electron Microscopy Image

To start off this article, I am going to assume that you have either seen/taken an electron microscopy (EM) image before or at the very least are familiar with electron microscopes. If not, please check out part 1 in my series where I detail the motivations behind developing this app. Let’s assume, though, that you are a researcher who has taken some EM measurements and now would like to perform some quantitative analysis on your images. More specifically, you would like to determine the mean size of the particles in your image and the standard deviation of that distribution. As an example, let’s say you have an EM image like the one seen in Figure 1 below.

Image for post

Fig. 1 An example EM image. source: CNR-IOM (CC-BY)

The first thing to note here is the banner that is displayed along the bottom portion of the image which contains information about the measurement such as the scale bar, its electron high tension (EHT) and its magnification. Many electron microscopes and its accompanying software will add this kind of information (at minimum there will be a scale bar) to the image. Unfortunately, since this is part of the image itself, leaving it in may affect the resulting segmentation from the deep learning model.

In order to reduce the potential for error, the additional “meta-information” should be removed from the image whenever possible. Take care to keep a record of the scale bar elsewhere, however, as it will be needed to convert the final calculation from pixels to a physical size in the final step. For now, the “meta-information” can be removed through a number of different methods.

The simplest method and the one I would personally recommend is to just crop it out of the image. It has the least potential to introduce further artifacts and requires the least technical prowess in image processing to perform. The only downside is that you may be losing important data by cropping the image.

In the interest of presenting other options, you can also use some more involved image processing techniques to remove the banner using either the open-cv or scikit-image libraries in Python. Some of these methods include using reflective padding, nearest neighbor padding, and constant padding. An example of all three methods are shown in Figure 2. The region where the banner used to be is highlighted in red in all three examples.

Image for post

Fig. 2 a) example of removing the banner using reflective padding b) example of removing the banner by using nearest neighbor padding c) removing the banner by replacing it with a constant padding. source: CNR-IOM (CC-BY)

As can be seen, each of these methods can result in unintended artifacts to the image and it is up to you to decide how you would like to deal with the “meta-information”.

#electron-microscopy #data-science #machine-learning #deep-learning #data analysis

I am Developer

1620289849

How to Compress Image Size In Codeigniter 4

Codeigniter compress image size. In this tutorial, you will learn how to upload and compress image size in codeigniter app.

This tutorial will guide you step by step on how to compress image size and upload in codeigniter app. And you can easily compress any image type like png, jpg, jpeg, gif etc.

How to Compress Image Size In CodeIgniter

Follow the following steps and you can easily compress image size in codeigniter app:

  • Download Codeigniter Latest
  • Basic Configurations
  • Create Database With Table
  • Setup Database Credentials
  • Create Controller
  • Create Views
  • Start Development server

https://www.tutsmake.com/codeigniter-4-image-size-compress-example/

#codeigniter compress image size #codeigniter compress image size example #codeigniter 4 compress image size #image resize in codeigniter

I am Developer

1597565398

Laravel 7/6 Image Validation

In this image validation in laravel 7/6, i will share with you how validate image and image file mime type like like jpeg, png, bmp, gif, svg, or webp before uploading image into database and server folder in laravel app.

https://www.tutsmake.com/image-validation-in-laravel/

#laravel image validation #image validation in laravel 7 #laravel image size validation #laravel image upload #laravel image validation max #laravel 6 image validation

I am Developer

1596033632

Image Validation In Laravel 7

Image validation in laravel. Here you will learn how to validate image and image mime type, size, and dimesion in laravel.

This tutorial will help you to validate image and image mime type like like jpeg, png, bmp, gif, svg, or webp before uploading to database and server folder in laravel app.

As well as, learn how to validate images mime type, file max size image dimension for image upload in laravel app.

This tutorial will guide you step by step to validate image in laravel with it’s size, mime type, and dimension in laravel app.

Laravel 7 Image Upload Validation

Follow the following steps and validate image mime type, size, and dimension before uploading to database and server folder in laravel app:

Step 1: Add routes
Step 2: Create Blade Views
Step 3: Add methods on Controller

Read full post https://www.tutsmake.com/image-validation-in-laravel/

#laravel image validation #image upload in laravel 7 #laravel image upload #image validation in laravel 6 #laravel+file upload validation #image size validation in laravel