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Saving 3D image after segmentation

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Aisha Al Ghurabi
Aisha Al Ghurabi le 20 Avr 2024
I have a 3D image rock that I preformed segmentation on using this code
RA = imread('BB258_6_A_2um_1600x3_8bit.tif');
threshold_calc = multithresh(RA, 2); %two is the number of thresholds so we are expecting to have 3 classes
image_segmented = imquantize(RA, threshold_calc);
imshow(image_segmented , []);
what I want to do is to save the 3D image as tif can you please help me

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Image Analyst
Image Analyst le 20 Avr 2024
Did you try imwrite or save?
help imwrite
IMWRITE Write image to graphics file. IMWRITE(A,FILENAME,FMT) writes the image A to the file specified by FILENAME in the format specified by FMT. A can be an M-by-N (grayscale image) or M-by-N-by-3 (color image) array. A cannot be an empty array. If the format specified is TIFF, IMWRITE can also accept an M-by-N-by-4 array containing color data that uses the CMYK color space. FILENAME is a character vector or string scalar that specifies the name of the file. FMT is a character vector or string scalar specifying the format of the file. See the reference page, or the output of the IMFORMATS function, for a list of supported formats. IMWRITE(X,MAP,FILENAME,FMT) writes the indexed image in X and its associated colormap MAP to FILENAME in the format specified by FMT. If X is of class uint8 or uint16, IMWRITE writes the actual values in the array to the file. If X is of class double, IMWRITE offsets the values in the array before writing, using uint8(X-1). MAP must be a valid MATLAB colormap. Note that most image file formats do not support colormaps with more than 256 entries. When writing multiframe GIF images, X should be an 4-dimensional M-by-N-by-1-by-P array, where P is the number of frames to write. IMWRITE(...,FILENAME) writes the image to FILENAME, inferring the format to use from the filename's extension. The extension must be one of the legal values for FMT. IMWRITE(...,PARAM1,VAL1,PARAM2,VAL2,...) specifies parameters that control various characteristics of the output file. Parameters are currently supported for GIF, HDF, JPEG, TIFF, PNG, PBM, PGM, and PPM files. IMWRITE(...,URL) writes image at a remote location. When writing data to remote locations, you must specify the full path using a uniform resource locator (URL). For example, to write an image from Amazon S3 cloud specify the full URL for the image: s3://bucketname/path_to_file/my_image.jpg IMWRITE(...,URL,'WriteMode','append') appends a frame to a TIF or GIF file at a remote location. When writing data to remote locations, you must specify the full path using a uniform resource locator (URL). For example, to write an image from Amazon S3 cloud specify the full URL for the image: s3://bucketname/path_to_file/my_image.jpg For more information on accessing remote data, see "Work with Remote Data" in the documentation. Class Support ------------- The input array A can be of class logical, uint8, uint16, single, or double. Indexed images (X) can be of class uint8, uint16, single, or double; the associated colormap, MAP, must be double. Input values must be full (non-sparse). The class of the image written to the file depends on the format specified. For most formats, if the input array is of class uint8, IMWRITE outputs the data as 8-bit values. If the input array is of class uint16 and the format supports 16-bit data (JPEG, PNG, and TIFF), IMWRITE outputs the data as 16-bit values. If the format does not support 16-bit values, IMWRITE issues an error. Several formats, such as JPEG and PNG, support a parameter that lets you specify the bit depth of the output data. If the input array is of class double, and the image is a grayscale or RGB color image, IMWRITE assumes the dynamic range is [0,1] and automatically scales the data by 255 before writing it to the file as 8-bit values. If the input array is of class double, and the image is an indexed image, IMWRITE converts the indices to zero-based indices by subtracting 1 from each element, and then writes the data as uint8. If the input array is of class logical, IMWRITE assumes the data is a binary image and writes it to the file with a bit depth of 1, if the format allows it. BMP, PNG, or TIFF formats accept binary images as input arrays. GIF-specific parameters ----------------------- 'WriteMode' One of these values: 'overwrite' (the default) or 'append'. In append mode, a single frame is added to the existing file. 'Comment' A character vector or cell array of character vector or string scalar or string array, containing a comment to be added to the image. For a cell array of character vector or string array, a carriage return is added after each row. 'DisposalMethod' One of the following values, which sets the disposal method of an animated GIF: 'leaveInPlace', 'restoreBG', 'restorePrevious', or 'doNotSpecify'. 'DelayTime' A scalar value between 0 and 655 inclusive, which specifies the delay in seconds before displaying the next image. 'TransparentColor' A scalar integer. This value specifies which index in the colormap should be treated as the transparent color for the image. If X is uint8 or logical, then indexing starts at 0. If X is double, then indexing starts at 1. 'BackgroundColor' A scalar integer. This value specifies which index in the colormap should be treated as the background color for the image and is used for certain disposal methods in animated GIFs. If X is uint8 or logical, then indexing starts at 0. If X is double, then indexing starts at 1. 'LoopCount' A finite integer between 0 and 65535 or the value Inf which specifies the number of times to repeat the animation after it is played once. If LoopCount is 0 (the default), then the animation is played once. If LoopCount is 1, then the animation is played twice, and so forth. If LoopCount is Inf, then the animation is played indefinitely. 'ScreenSize' A two element vector specifying the screen height and width of the frame. When used with 'Location', this provides a way to write frames to the image which are smaller than the whole frame. The remaining values are filled in according to the 'DisposalMethod'. 'Location' A two element vector specifying the offset of the top left corner of the screen relative to the top left corner of the image. The first element is the offset from the top, and the second element is the offset from the left. HDF-specific parameters ----------------------- 'Compression' One of these values: 'none' (the default), 'rle' (only valid for grayscale and indexed images), 'jpeg' (only valid for grayscale and RGB images) 'Quality' A number between 0 and 100; parameter applies only if 'Compression' is 'jpeg'; higher numbers mean quality is better (less image degradation due to compression), but the resulting file size is larger 'WriteMode' One of these values: 'overwrite' (the default) or 'append' JPEG-specific parameters ------------------------ 'Quality' A number between 0 and 100; higher numbers mean quality is better (less image degradation due to compression), but the resulting file size is larger 'Comment' Comment must be a column containing text specified as chars, strings, cell array of character vectors, or string array. Each row of input is written out as a comment in the JPEG file. 'Mode' Either 'lossy' (the default) or 'lossless' 'BitDepth' A scalar value indicating desired bitdepth; for grayscale images this can be 8, 12, or 16; for truecolor images this can be 8 or 12. Only lossless mode is supported for 16-bit images. JPEG2000-specific parameters ---------------------------- 'Mode' Either 'lossy' (the default) or 'lossless'. 'CompressionRatio' A real value greater than 1 specifying the target compression ratio which is defined as the ratio of input image size to the output compressed size. For example, a value of 2.0 implies that the output image size will be half of the input image size or less. A higher value implies a smaller file size and reduced image quality. This is valid only with 'lossy' mode. Note that the compression ratio doesn't take into account the header size, and hence in some cases the output file size can be larger than expected. 'ProgressionOrder' A character vector or string scalar that is one of 'LRCP', 'RLCP', 'RPCL', 'PCRL' or 'CPRL'. The four character identifiers are interpreted as L=layer, R=resolution, C=component and P=position. The first character refers to the index which progresses most slowly, while the last refers to the index which progresses most quickly. The default value is 'LRCP'. 'QualityLayers' A positive integer (not exceeding 20) specifying the number of quality layers. The default value is 1. 'ReductionLevels' A positive integer (not exceeding 8) specifying the number of reduction levels or the wavelet decomposition levels. 'TileSize' A 2-element vector specifying tile height and tile width. The minimum tile size that can be specified is [128 128]. The default tile size is same as the image size. 'Comment' Comment must be a column containing text specified as chars, strings, cell array of character vectors, or string array. Each row of input is written out as a comment in the JPEG2000 file. TIFF-specific parameters ------------------------ 'Colorspace' One of these values: 'rgb', 'cielab', or 'icclab'. The default value is 'rgb'. This parameter is used only when the input array, A, is M-by-N-by-3. See the reference page for more details about creating L*a*b* TIFF files. In order to create a CMYK TIFF, the colorspace parameter should not be used. It is sufficient to specify the input array A as M-by-N-by-4. 'Compression' One of these values: 'none', 'packbits' (default for nonbinary images), 'lzw', 'deflate', 'jpeg', 'ccitt' (default for binary images), 'fax3', 'fax4'; 'ccitt', 'fax3', and 'fax4' are valid for binary images only. 'jpeg' is a lossy compression scheme; other compression modes are lossless. When using JPEG compression, the 'RowsPerStrip' parameter must be specified and must be a multiple of 8. 'Description' Any character vector or string scalar; fills in the ImageDescription field returned by IMFINFO 'Resolution' A two-element vector containing the XResolution and YResolution, or a scalar indicating both resolutions; the default value is 72 'RowsPerStrip' A scalar value. The default will be such that each strip is about 8K bytes. 'WriteMode' One of these values: 'overwrite' (the default) or 'append' PNG-specific parameters ----------------------- 'Author' A character vector or string scalar 'Description' A character vector or string scalar 'Copyright' A character vector or string scalar 'CreationTime' A character vector or string scalar 'ImageModTime' A MATLAB datenum or a character vector or string scalar convertible to a date vector via the DATEVEC function. Values should be in UTC time. 'Software' A character vector or string scalar 'Disclaimer' A character vector or string scalar 'Warning' A character vector or string scalar 'Source' A character vector or string scalar 'Comment' A character vector or string scalar 'InterlaceType' Either 'none' or 'adam7' 'BitDepth' A scalar value indicating desired bitdepth; for grayscale images this can be 1, 2, 4, 8, or 16; for grayscale images with an alpha channel this can be 8 or 16; for indexed images this can be 1, 2, 4, or 8; for truecolor images with or without an alpha channel this can be 8 or 16 'Transparency' This value is used to indicate transparency information when no alpha channel is used. For indexed images: a Q-element vector in the range [0,1]; Q is no larger than the colormap length; each value indicates the transparency associated with the corresponding colormap entry For grayscale images: a scalar in the range [0,1]; the value indicates the grayscale color to be considered transparent For truecolor images: a 3-element vector in the range [0,1]; the value indicates the truecolor color to be considered transparent You cannot specify 'Transparency' and 'Alpha' at the same time. 'Background' The value specifies background color to be used when compositing transparent pixels. For indexed images: an integer in the range [1,P], where P is the colormap length For grayscale images: a scalar in the range [0,1] For truecolor images: a 3-element vector in the range [0,1] 'Gamma' A nonnegative scalar indicating the file gamma 'Chromaticities' An 8-element vector [wx wy rx ry gx gy bx by] that specifies the reference white point and the primary chromaticities 'XResolution' A scalar indicating the number of pixels/unit in the horizontal direction 'YResolution' A scalar indicating the number of pixels/unit in the vertical direction 'ResolutionUnit' Either 'unknown' or 'meter' 'Alpha' A matrix specifying the transparency of each pixel individually; the row and column dimensions must be the same as the data array; may be uint8, uint16, or double, in which case the values should be in the range [0,1] 'SignificantBits' A scalar or vector indicating how many bits in the data array should be regarded as significant; values must be in the range [1,bitdepth] For indexed images: a 3-element vector For grayscale images: a scalar For grayscale images with an alpha channel: a 2-element vector For truecolor images: a 3-element vector For truecolor images with an alpha channel: a 4-element vector In addition to these PNG parameters, you can use any parameter name that satisfies the PNG specification for keywords: only printable characters, 80 characters or fewer, and no leading or trailing spaces. The value corresponding to these user-specified parameters must be a character vector or string scalar that contains no control characters except for linefeed. RAS-specific parameters ----------------------- 'Type' One of these values: 'standard' (uncompressed, b-g-r color order with truecolor images), 'rgb' (like 'standard', but uses r-g-b color order for truecolor images), 'rle' (run-length encoding of 1-bit and 8-bit images) 'Alpha' A matrix specifying the transparency of each pixel individually; the row and column dimensions must be the same as the data array; may be uint8, uint16, or double. May only be used with truecolor images. PBM, PGM, and PPM-specific parameters ------------------------ 'Encoding' One of these values: 'ASCII' for plain encoding or 'rawbits' for binary encoding. Default is 'rawbits'. 'MaxValue' A scalar indicating the maximum gray or color value. Available only for PGM and PPM files. For PBM files, this value is always 1. Default is 65535 if image array is 'uint16' and 255 otherwise. Table: summary of supported image types --------------------------------------- BMP 1-bit, 8-bit and 24-bit uncompressed images GIF 8-bit images HDF 8-bit raster image datasets, with or without associated colormap; 24-bit raster image datasets; uncompressed or with RLE or JPEG compression JPEG 8-bit, 12-bit, and 16-bit Baseline JPEG images JPEG2000 1-bit, 8-bit, and 16-bit JPEG2000 images PBM Any 1-bit PBM image, ASCII (plain) or raw (binary) encoding. PCX 8-bit images PGM Any standard PGM image. ASCII (plain) encoded with arbitrary color depth. Raw (binary) encoded with up to 16 bits per gray value. PNG 1-bit, 2-bit, 4-bit, 8-bit, and 16-bit grayscale images; 8-bit and 16-bit grayscale images with alpha channels; 1-bit, 2-bit, 4-bit, and 8-bit indexed images; 24-bit and 48-bit truecolor images; 24-bit and 48-bit truecolor images with alpha channels PNM Any of PPM/PGM/PBM (see above) chosen automatically. PPM Any standard PPM image. ASCII (plain) encoded with arbitrary color depth. Raw (binary) encoded with up to 16 bits per color component. RAS Any RAS image, including 1-bit bitmap, 8-bit indexed, 24-bit truecolor and 32-bit truecolor with alpha. TIFF Baseline TIFF images, including 1-bit, 8-bit, 16-bit, and 24-bit uncompressed images, images with packbits compression, images with LZW compression, and images with Deflate compression; 8-bit and 24-bit images with JPEG compression; 1-bit images with CCITT 1D, Group 3, and Group 4 compression; CIELAB, ICCLAB, and CMYK images. XWD 8-bit ZPixmaps Please read the file libtiffcopyright.txt for more information. See also IMFINFO, IMREAD, IMFORMATS, FWRITE, GETFRAME. Documentation for imwrite doc imwrite Other uses of imwrite gpuArray/imwrite
  3 commentaires
Image Analyst
Image Analyst le 22 Avr 2024
Was your original RA a 3D array? So if imwrite can't save your data as 3-D, try Tiff because that has more options for TIFF files whan imwrite does.
Aisha Al Ghurabi
Aisha Al Ghurabi le 23 Avr 2024
thank you but I got the answer , I had just to rescale the image Aoutput = uint8((255 / 3) * outputImage); and then use squeeze function in the loop to get it as 3D

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Matt J
Matt J le 21 Avr 2024
There are several File Exchange submissions that are applicable. I have used this one and been pretty happy,

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