FracTile Compiler Instructions Currently supported web browsers: Firefox and Chrome ---------------------------------------------------- Table of Contents and Brief Summary of Tabs [1] Select Canvas (changes canvas size and resolution) [2] Upload Image (auto chooses points in conjuction with the Modify Layout tab) [3] Modify Layout (Tools for selecting pixel location manually or from an uploaded image) [4] Abstract Tiles (Abstract level visual render format demonstrating edge identities) [5] DNA Origami Tiles (DNA level render of the origiami layout itself) [6] Sequences & Protocols (all DNA strands necessary and mixing protocols for the inputted design) [7] Mock AFM Image (Sets parameters under "Modify Layout" to colors mimmicking standard false-color AFM images) [8] Save Layout & Images (assorted save options) [9] Load Layout [10] Example Images and Layout (assorted examples) ---------------------------------------------------- [1] Select Canvas Hover mouse over tab to open a drop down menu 1) Select the Canvas Size 4 radio buttons will show up (1x1, 2x2, 4x4, and 8x8) with 8x8 selected by default. This is the size of the origami array (ie 8 by 8 origami for 64 total origami squares) Click on a radio button to reset the canvas to the desired size (Note: it will clear any selected pixels) 2) Select the Resolution One number input box representing the pixel resolution of the display Nx2N (Note: 2N due included space for an uploaded image) Change number than press "Enter/Return" on your keyboard to register the changed value The value may be increased to make a sharper image for downloading [2] Upload Image 1) Click on tab to open a choose file prompt 2) Select desired image (ie .jpg, .png, etc) Image will be auto-converted to grayscale Use lower resolution black/white images for best results Initual threshold for automatic pixel selection is 100/255 with the grayscale image pixel range set to 0-255. The threshold and other parameters can be changed under the "Modify Layout" tab [3] Modify Layout Hover mouse over tab to open a drop down menu 1) Manual Editing/Drawing Tools Select Dots - Click to have mouse clicks on the canvas turn nearby pixel(s) to selected pixels (Default active) Remove Dots - Click to have mouse clicks on the canvas turn nearby pixel(s) to non-selected pixels Select Quantity - Modify value in the box (then press "Enter/Return") to choose # of nearby pixels selected/removed by above clicks 2) Uploaded Image tools Invert - Check box to flip selected and non-selected pixels Set Uploaded Image Threshold - Modify value in box (press "Enter/Return") from 0-255; sets theshold used in auto-pixel picking Shift Image X:_ Y:_ - Modify values to shift uploaded image X,Y pixels relative to the canvas (then press "Enter/Return") Useful to move key features away from origami edge seams Can be negative values Scale Image X:_ Y:_ - Moidfy values to scale uploaded image's width,height relative to the canvas (then press "Enter/Return") Shift Color Default - When shifting image out of the frame, what deafult fill should be used on the canvas 3) Canvas Colors and Appearance; Modify value in box (press "Enter/Return") Canvas Pixel Size: Sets non-selected pixel diameter Select Pixel Size: Sets selected pixel diameter Canvas Pixel Color: Sets non-selected pixel color #RRGGBB Select Pixel Color: Sets selected pixel color #RRGGBB Background Color: Sets color behind all the pixels (default white #ffffff) [4] Abstract Tiles Click on tab to begin Image render Note: A large resolution may take some time on a slow computer You can click on "Select Canvas" or "Modify layout" tabs to return to the Canvas draw view [5] DNA Origami Tiles Click on tab to begin Image render Note: A large resolution may take some time on a slow computer You can click on "Select Canvas" or "Modify layout" tabs to return to the Canvas draw view [6] Sequences & Protocols Click on tab to open list of sequences and protocols 1) DNA Sequences (Left List) - list of all strands needed to design any pattern and array size Click on "Save Sequences" button below the list to download the list (or copy directly from the list) 2) Manual Protocol (Right List) - Layout of a mixing protocol using the above strands Strand Mixes are defined for a global bridge mix, then individual tile's edges and internal strand mixes Finally annealing schedules are supplied Click on "Save Manual Protocol" button below the list to download the list (or copy directly from the list) Click on "Save Labcyte Echo Input Protocol" for an input protocol for a Labcyte Echo automatic liquid handler Click on "Save Labcyte Echo Plate Layout" for an input plate layout for all DNA strands in the above automatic Echo Protocol [7] Mock AFM Image Click tab to set parameters under "Modify Layout" to colors mimmicking standard false-color AFM images Normal Colors: Canvas Pixel Color: #888888 Select Pixel Color: #000000 Background Color: #ffffff AFM Colors: Canvas Pixel Color: #834400 Select Pixel Color: #cfb980 Background Color: #1e0000 [8] Save Layout & Images Hover mouse over tab to open a drop down menu 1) Save Layout - put name of desired layout file "example.txt", click "Save Layout" Saves the currently selected pixel layout for later loading (see "Load Layout") 2) Save Images Save SVG - saves an SVG of the current full canvas SVG Canvas - saves an SVG of cavnas pixels SVG Select - saves an SVG of Selected pixels "temp.svg" - modify to desired downloaded SVG file name Save PNG - saves a PNG of cavnas and uploaded image "temp.png" - modify to desired downloaded PNG file name Pixels Nx[2N]: modify to desired resoltuion of downloaded image [9] Load Layout 1) Click on tab to open a choose file prompt 2) Open a saved "Layout File" (ie "temp.txt") 3) the saved canvas should open [10] Example Images and Layout Hover mouse over tab to open a drop down menu Click and see for yourself! Thanks for using the FracTile Compiler!