Moving Map Manager files to another folder or computer

If you want to move your analysis into a different folder or a different computer, please follow these simple rules

Moving a single-time point analysis

  • Move the original .tif stack along with its associated _db2.txt, _int1.txt, _int2.txt, and _l.txt files contained in the enclosed ‘stackdb’ folder.

Moving a map analysis

  • Move the main map file .ibw and its folder to a new location or computer.

Reading Map Manager files in other programming environments

Map Manager saves all stack and time-series map files as plain text files. In this way, annotations created in Map Manager can easily be opened in a wide range of other programming environments for additional visualization and analysis.

We provide a Python package, PyMapManager, to do this. Please have a look at this package as a starting point for custom analysis and visualization using existing Map Manager files.

If you are on a Mac, python comes pre-installed and you are good to go. In general, Anaconda is a useful starting point as it pre-installes most Python packages you might need. Download Anaconda here.

Map Manager file format

For the intrepid data scientist (e.g. data analyst) we are providing the details of the Map Manager file format for both single time-points and maps. If you want to get started importing these files into Matlab, please contact Robert Cudmore and we can share some rudimentary code snippets to read these files. Again, we strongly suggest you get started with the PyMapManager Python package.

Single time-point files

  • The original .tif file is never modified
  • Annotations are saved in a stackdb folder
    • db2
    • int1
    • int2
    • line

stackdb

int1 and int2

line

Map files

  • Maps are saved in a folder whose name is the same as the map name
  • At the root of this folder are three map files
    • map. see format
    • object map
    • segment map (if there are segment)
  • There are some folders
    • line
    • raw: The original .tif files are never modified, these are direct copies.
    • stackdb

map

object map

segment map

stack db

line

[FUTURE] HDF5

HDF5 is an open source cross platform binary file format. It can be read from Matlab, Python, Igor Pro and from a command line.

Out of the box, Map Manager is not saving files in the HDF5 format. If you are interested in turning on this feature, please email Robert Cudmore.

Each file has the following format

Map file format

index 0 1 2 3 4 5 6 7 8
hsType mm3 mm3 mm3 mm3 mm3 mm3 mm3 mm3 mm3
hsStack rr30a_s0 rr30a_s1 rr30a_s2 rr30a_s3 rr30a_s4 rr30a_s5 rr30a_s6 rr30a_s7 rr30a_s8
hsdb rr30a_s0_db2 rr30a_s1_db2 rr30a_s2_db2 rr30a_s3_db2 rr30a_s4_db2 rr30a_s5_db2 rr30a_s6_db2 rr30a_s7_db2 rr30a_s8_db2
hsStackNV rr30a_s0 rr30a_s1 rr30a_s2 rr30a_s3 rr30a_s4 rr30a_s5 rr30a_s6 rr30a_s7 rr30a_s8
date 20141009 20141013 20141016 20141017 20141018 20141020 20141021 20141022 20141029
time 20:01:40 22:24:04 19:49:05 20:30:39 16:18:59 19:25:41 18:36:19 19:47:00 19:05:27
hsStackSeconds 3495729700 3496083844 3496333745 3496422639 3496493939 3496677941 3496761379 3496852020 3497454327
fiducPnt 0 0 0 0 0 0 0 0 0
numChannels 2 2 2 2 2 2 2 2 2
defaultChannel 2 2 2 2 2 2 2 2 2
px 1024 1024 1024 1024 1024 1024 1024 1024 1024
py 1024 1024 1024 1024 1024 1024 1024 1024 1024
pz 70 65 70 70 70 80 70 80 70
dx 0.12 0.12 0.12 0.12 0.12 0.12 0.12 0.12 0.12
dy 0.12 0.12 0.12 0.12 0.12 0.12 0.12 0.12 0.12
dz 1 1 1 1 1 1 1 1 1
stackdbVersion 20151224                
numSeg 5                
numObj 2467                
numSpine 1227                
importedStackName RR30a_S0 RR30a_S1 RR30a_S2 RR30a_S3 RR30a_S4 RR30a_S5 RR30a_S6 RR30a_S7 RR30a_S8
condStr a1 a2 e b1 b2 b c1 c2 c3
zeroSession 0                
sessions 0 1 2 3 4 5 6 7 8
datetime 3495729700 3496083844 3496333745 3496422639 3496493939 3496677941 3496761379 3496852020 3497454327
days 0 4.0989 6.9913 8.0201 8.8454 10.975 11.941 12.99 19.961
hours 0 98.373 167.79 192.48 212.29 263.4 286.58 311.76 479.06
zsessions 0 1 2 3 4 5 6 7 8
zdays 0 4.0989 6.9913 8.0201 8.8454 10.975 11.941 12.99 19.961
zhours 0 98.373 167.79 192.48 212.29 263.4 286.58 311.76 479.06
mapCond mc1